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672c882ef9980725cf6d6ca9 | 10.26434/chemrxiv-2024-dl4jj-v2 | Impact of Magnetic Ion Substitution on the Crystal Structure of Multiferroic Aurivillius Phases | The five-layered (m = 5) Bi6Ti2.99Fe1.46Mn0.55O18 Aurivillius material is a rare example of a single-phase room temperature ferroelectric-ferrimagnetic multiferroic that shows promise for energy-efficient memory devices. Its ferrimagnetism is thought to derive from the natural partitioning of magnetic ions to the central perovskite layer, engendered by chemically-driven lattice strains, together with ferromagnetic coupling via superexchange mechanisms. Motivated by the expectation of an enhancement in magnetization with increased magnetic ion content, this study examines systematic B-site substitutions with the aim of increasing (from the current level of 40%) the proportion of magnetic ions within the structure. The solubility limits of magnetic cations in this structure and their influence on the superlattice layering are investigated. Studies of Aurivillius phase films on c-sapphire with composition Bi6TixFeyMnzO18 (B6TFMO; x = 2.3 to 3.2, y = 1.2 to 2.0, z = 0.3 to 0.9) demonstrated that above ca. 46% of B-site magnetic cations, the m = 5 structure first rearranges into a mixed-phase material based on m = 5 and six-layered (m = 6) structures and eventually evolves into an m = 6 phase with 54% magnetic cations at the B-site. It is postulated that increasing the number of perovskite layers by forming the m = 6 structure facilitates the accommodation of additional magnetic cations at a lower average manganese oxidation state (+3.3) compared with an equivalent m = 5 stoichiometry (+4.0). While the minor out-of-plane ferroelectric response decreases as expected with increasing structural reorganization towards the m = 6 phase, the predominant in-plane piezoresponse remains unaffected by magnetic cation substitution. This work shows that higher-layered Aurivillius homologues can be synthesized using aliovalent substitution, without requiring epitaxial growth or kinetically constrained methods. | Jennifer Halpin; Michael Schmidt; Roger W. Whatmore; Lynette Keeney | Materials Science; Inorganic Chemistry; Materials Processing; Nanostructured Materials - Materials; Thin Films; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672c882ef9980725cf6d6ca9/original/impact-of-magnetic-ion-substitution-on-the-crystal-structure-of-multiferroic-aurivillius-phases.pdf |
65b9ff9066c1381729a1c33e | 10.26434/chemrxiv-2024-ssbxj | Exploring the Aggregation Propensity of PHF6 Peptide Segments of the Tau Protein using Ion Mobility Mass Spectrometry Techniques | Peptide and protein aggregation involves the formation of oligomeric species, but the complex interplay between oligomers of different conformations and sizes complicates their structural elucidation. Using ion mobility mass spectrometry (IM-MS), we aim to reveal these early steps of aggregation for the Ac-PHF6-NH2 peptide segment from tau protein, thereby distinguishing between different oligomeric species, and gaining an understanding of the aggregation pathway. An important factor that is often neglected, but which can alter the aggregation propensity of peptides, is the terminal capping groups. Here we demonstrate the use of IM-MS to probe the early stages of aggregate formation of the Ac-PHF6-NH2, Ac-PHF6, PHF6-NH2, and uncapped PHF6 peptide segments. The aggregation propensity of the four PHF6 segments is confirmed using thioflavin T fluorescence assays and transmission electron microscopy. Post-IM fragmentation and quadrupole selection on the TIMS-Qq-ToF (trapped ion mobility) spectrometer are introduced to improve oligomer assignment. In addition, TIMS collision cross section values are compared with travelling wave ion mobility (TWIMS) data to evaluate potential instrumental bias in the trapped ion mobility results. The two IM-MS instrumental platforms are based on different ion mobility principles and have different configurations, thereby providing us with valuable insight into the preservation of weakly bound biomolecular complexes such as peptide aggregates | Iuliia Stroganova; Hannah Willenberg; Thaleia Tente; Agathe Depraz Depland; Sjors Bakels; Anouk Rijs | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b9ff9066c1381729a1c33e/original/exploring-the-aggregation-propensity-of-phf6-peptide-segments-of-the-tau-protein-using-ion-mobility-mass-spectrometry-techniques.pdf |
65995572e9ebbb4db98d9365 | 10.26434/chemrxiv-2024-31c4q | Ruthenium catalyst with a planar-chiral arene ligand: synthesis, separation of enantiomers, and application in C-H activation of N-methoxy-benzamides | Heating tert-butyl-tetraline with [(p-cymene)RuCl2]2 produces the racemic complex [(arene)RuCl2]2, which can be separated into enantiomers by chromatography of its diastereomeric adducts with chiral phosphine ligand. The resolved chiral complex catalyzes C-H activation of N-methoxy-benzamides and their annulation with N-vinyl-pivaloyl amide giving dihydroisoquinolones in 50-90% yields and 70:30-90:10 enantiomeric ratio. | Mikhail Boym; Roman Pototskiy; Evgeniya Podyacheva; Denis Chusov; Yulia Nelyubina; Dmitry Perekalin | Catalysis; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65995572e9ebbb4db98d9365/original/ruthenium-catalyst-with-a-planar-chiral-arene-ligand-synthesis-separation-of-enantiomers-and-application-in-c-h-activation-of-n-methoxy-benzamides.pdf |
659c059fe9ebbb4db9b19459 | 10.26434/chemrxiv-2023-7hntk-v3 | Substituting density functional theory in reaction barrier calculations for hydrogen atom transfer in proteins | Hydrogen atom transfer (HAT) reactions are important in many biological systems. As these reactions are hard to observe experimentally, it is of high interest to shed light on them using simulations. Here, we present a machine learning model based on graph neural networks for the prediction of energy barriers of HAT reactions in proteins. As input, the model uses exclusively non-optimized structures as obtained from classical simulations. It was trained on more than 17,000 energy barriers calculated using hybrid density functional theory. We built and evaluated the model in the context of HAT in collagen, but we show that the same workflow can easily be applied to HAT reactions in other biological or synthetic polymers. We obtain for relevant reactions (small reaction distances) a model with good predictive power (R2 ∼ 0.9 and mean absolute error of < 3 kcal/mol). As the inference speed is high, this model enables evaluations of dozens of chemical situations within seconds. When combined with molecular dynamics in a kinetic Monte-Carlo scheme, the model paves the way toward reactive simulations. | Kai Riedmiller; Patrick Reiser; Elizaveta Bobkova; Kiril Maltsev; Ganna Gryn'ova; Pascal Friederich; Frauke Gräter | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659c059fe9ebbb4db9b19459/original/substituting-density-functional-theory-in-reaction-barrier-calculations-for-hydrogen-atom-transfer-in-proteins.pdf |
674dda0c7be152b1d0b13870 | 10.26434/chemrxiv-2024-4vh9g | Heteroatom-Substituted Re-Flashed Graphene | Flash Joule heating is an ultrafast, energy-efficient, and scalable technique used in the production of a variety of organic and inorganic compounds, including flash graphene. This technique has also been used in the production of doped graphene by flash Joule heating amorphous carbon in the presence of heteroatom-donating compounds. Herein, we report a modified flash Joule heating technique by which graphene is formed with up to 21 at% of the graphene lattice containing substituted heteroatoms. This is achieved by re-flashing graphene in the presence of heteroatom-donating compounds, allowing this substitution to occur at lower temperatures than previously reported for flash Joule heating-synthesized doped graphene and thereby permitting much higher amounts of heteroatom insertion into the graphene lattice. We demonstrate nitrogen, sulfur, phosphorus, and fluorine atom atomic substitution into or upon the graphene lattice, as well as multi-heteroatom substitution. Finally, the implementation of the nitrogen-substituted re-flashed graphene into battery anodes exhibits improved performance and stability relative to unsubstituted re-flashed graphene battery anodes. | Phelecia Scotland; Lucas Eddy; Jinhang Chen; Weiyin Chen; Jacob Beckham; Chi Choi; Paul Advincula; Kevin Wyss; Paul Savas; Lorenzo Castelli; Alexander Lathem; Obinna Onah; Geoff Wehmeyer; Yimo Han; James Tour | Organic Chemistry; Energy; Organic Synthesis and Reactions; Physical Organic Chemistry; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674dda0c7be152b1d0b13870/original/heteroatom-substituted-re-flashed-graphene.pdf |
62b3333e1672a283954898cf | 10.26434/chemrxiv-2022-727kf-v2 | Photoinduced charge transfer from quantum dots measured by cyclic voltammetry | Measuring and modulating charge-transfer processes at quantum dot interfaces are crucial steps in developing quantum dots as photocatalysts. In this work, cyclic voltammetry under illumination is demonstrated to measure the rate of photoinduced charge transfer from CdS quantum dots by directly probing the changing oxidation states of a library of molecular charge acceptors, including both hole and electron acceptors. The voltammetry data demonstrates the presence of long-lived charge donor states generated by native photodoping of the quantum dots as well as a positive correlation between driving force and rate of charge transfer. Changes to the voltammograms under illumination follow mechanistic predictions from classic zone diagrams and electrochemical modeling allows for measurement of the rate of productive electron transfer. Observed rates for photoinduced charge transfer on the order of 0.1 s-1 are calculated, which are distinct from the picosecond dynamics measured by conventional transient optical spectroscopy methods and are more closely connected to the quantum yield of light mediated chemical transformations. | Micaela Homer; Ding-Yuan Kuo; Florence Dou; Brandi Cossairt | Physical Chemistry; Inorganic Chemistry; Nanoscience; Electrochemistry; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b3333e1672a283954898cf/original/photoinduced-charge-transfer-from-quantum-dots-measured-by-cyclic-voltammetry.pdf |
6459d9271ca6101a4505d497 | 10.26434/chemrxiv-2023-n6xsl | Structural and Electronic Characterization of m-Fluoroaniline and m-Iodoaniline: A Density Functional Theory Study | This study aimed to investigate the electronic and structural characteristics of m-fluoroaniline (MFA) and m-iodoaniline (MIA). Density functional theory (DFT) and CAM-B3LYP/LanL2DZ methods were employed to determine various properties such as the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels, chemical reactivity descriptors, nonlinear optical properties, Mulliken population analysis, molecular electrostatic potential map, thermodynamic properties, and UV-Vis spectral analysis. In addition, the research explored the vertical and adiabatic ionization energy parameters of these molecules by constructing singly charged cation radicals using the same level theory. The obtained results were compared with experimental data from the literature. | Yavuz Ekincioğlu; Abdullah KEPCEOĞLU | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6459d9271ca6101a4505d497/original/structural-and-electronic-characterization-of-m-fluoroaniline-and-m-iodoaniline-a-density-functional-theory-study.pdf |
60c75321469df408d6f44cba | 10.26434/chemrxiv.13401173.v1 | Microwave-Assisted Xylanase Reaction: The Impact in the Production of Prebiotic Xylooligosaccharides | The enzymatic production of prebiotic
xylooligosaccharides (XOS) has become an attractive way to valorize
lignocellulosic biomass. However, despite numerous xylanases reported for
potential use in the production of XOS, most of the family GH10 also produce
xylose. This monosaccharide can negatively affect the selectivity to stimulate
the growth of intestinal microorganisms beneficial to human health. In this work, a thermostable alkali-tolerant
xylanase (<i>Bh</i>Xyn10A) from <i>Bacillus
halodurans</i> S7 has been used to produce XOS under conventional convective
heat transfer and microwave radiation. The microwave–assisted reaction markedly
decreases the xylose content in the hydrolysates and significantly increases
the yield of XOS, compared to conventional heating. Molecular dynamic
simulations of <i>Bh</i>Xyn10A have shown an increased fluctuation of the amino
acids of the aglycone subsites suggesting that these subsites can determine the
production of xylose. Thus, the microwave heating could affect the amino acid
fluctuations in the aglycone subsites reducing the xylose formation. These
findings open up new avenues in enzyme technology for the production of XOS. | Hugo Mobarec; Rodrigo Villagomez; Eva Nordberg Karlsson; Javier Linares-Pastén | Biochemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75321469df408d6f44cba/original/microwave-assisted-xylanase-reaction-the-impact-in-the-production-of-prebiotic-xylooligosaccharides.pdf |
66cfed2ef3f4b052906fa85b | 10.26434/chemrxiv-2024-hnl71 | Chemoenzymatic synthesis planning by evaluating the synthetic potential in biocatalysis and chemocatalysis | Chemoenzymatic synthesis integrates the advantages of chemocatalysis and biocatalysis to design efficient synthesis routes. However, current computer-assisted chemoenzymatic synthesis planning tools lack a heuristic method to unify step-by-step chemoenzymatic synthesis planning and molecule-by-molecule identification of chemo-/biocatalysis opportunities in synthesis routes. Here we develop an asynchronous chemoenzymatic retrosynthesis planning algorithm (ACERetro) which employs a search strategy that prioritizes the exploration of a molecule's promising catalytic methods. The suitability of a molecule to be synthesized via chemo- or biocatalysis is quantitatively evaluated by a data-driven Synthetic Potential Score (SPScore) using a neural network model. Additionally, the SPScore can be used to heuristically identify chemo-/biocatalysis opportunities in synthesis routes. For a given synthesis route, this algorithm uses SPScore to identify the molecules that offer optimization potential when synthesized by an alternative catalytic method, and then ACERetro is used to search synthesis routes. Case studies on synthesis planning for ethambutol and epidiolex demonstrate that our strategy can design concise chemoenzymatic synthesis routes by applying enzymatic steps to introduce stereochemistry and find shortcuts. Moreover, case studies on synthesis route optimization for rivastigmine and (R,R)-formoterol demonstrate how our strategy finds bypasses to form alternative, shorter chemoenzymatic synthesis routes. Our findings demonstrate that ACERetro with evaluating the synthetic potential of molecules represents a versatile and effective search framework for chemoenzymatic synthesis planning. | Xuan Liu; Hongxiang Li; Huimin Zhao | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cfed2ef3f4b052906fa85b/original/chemoenzymatic-synthesis-planning-by-evaluating-the-synthetic-potential-in-biocatalysis-and-chemocatalysis.pdf |
60c758cfee301c5a0ec7b7c9 | 10.26434/chemrxiv.14610261.v1 | APP-C31 Is an Intracellular Promoter of Amyloid-Beta Aggregation and Toxicity | <p>Intracellular <i>C</i>-terminal cleavage of the amyloid precursor protein (APP) is elevated in the brain of Alzheimer’s disease (AD). Emerging evidence proposes a pathological relationship between the production of a <i>C</i>-terminal APP fragment, called APP-C31, and the toxicity induced by amyloid-beta (Abeta) that is a major contributor towards AD; however, the interaction between the two peptides and the consequent impact of APP-C31 on Abeta-related toxicity were unknown thus far. Here we report the discovery that APP-C31 facilitates the aggregation of Abeta and aggravates its toxicity at the intracellular level, with escalating neurodegeneration. APP-C31 forms a hetero-dimer with Abeta through the contacts onto the <i>N</i>-terminal and self-recognition regions of Abeta and induces its conformational transition accelerating amyloid fibrillization. APP-C31 promotes the perinuclear and intranuclear deposition of enlarged Abeta aggregates and, consequently, damages the nucleus leading to apoptosis. Abeta-induced degeneration of neurites in human neurons is also intensified by APP-C31. Our studies demonstrate a new function of APP-C31 as an intracellular factor of the proteopathy found in AD.</p> | Eunju Nam; Jiyong Park; Yuxi Lin; Hyunsu Do; Jinju Han; Young Ho Lee; Mu-Hyun Baik; Mi Hee Lim | Bioinorganic Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758cfee301c5a0ec7b7c9/original/app-c31-is-an-intracellular-promoter-of-amyloid-beta-aggregation-and-toxicity.pdf |
60c7555cee301c26e1c7b18b | 10.26434/chemrxiv.14096065.v1 | Non-reductive Homolytic Scission of Endoperoxide Bond for Activation of Artemisinin: The Bi-radical Perspectives | <p>Artemisinin is the most famous antimalarial drug against malaria caused by <i>Plasmodium falciparum</i>. Despite its
tremendous success and popularity in malaria therapeutics, the molecular
mechanism of artemisinin’s activity is still elusive. The activation of
artemisinin, i.e., cleavage of the endoperoxide bond at the infected cell that
generates radical intermediates and the subsequent chemical rearrangements plays a key role in the antimalarial activities. In this work, applying state-of-the-art
computational techniques based on the spin constraint density functional theory (CDFT) along with <i>ab initio</i> thermodynamics, we have
investigated various key steps of the
molecular mechanism of artemisinin. The well-accepted artemisinin activation
process is the reductive heterolytic scission of the endo-peroxide bond which
is followed by subsequent chemical reactions
that propagate via mono-radical intermediates. Here
adopting the CDFT we
have investigated the possible alternative ‘biradical’ intermediates and their mechanistic pathways for the subsequent
chemical reactions. The change in Gibbs free
energy associated with the activation of artemisinin through
homolytic-scissoring (biradical) intermediate is quite competitive and
favorable compared to the reductive heterolytic-scissoring (monoradical)
process. This clearly indicates the alternative possibilities for the biradical
activation process. The reported experimental EPR signals
for the biradicals especially for similar anti-malarial drugs like G3-factor support
our observations. </p> | Shikha Sharma; Md. Ehesan Ali | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7555cee301c26e1c7b18b/original/non-reductive-homolytic-scission-of-endoperoxide-bond-for-activation-of-artemisinin-the-bi-radical-perspectives.pdf |
628b860770876776975c9e43 | 10.26434/chemrxiv-2022-8vv6t | A Local Hybrid Exchange Functional Approximation from First Principles | Local hybrid functionals are a more flexible class of density functional approximations allowing for a position-dependent admixture of exact exchange. This additional flexibility, however, comes with a more involved mathematical form and a more complicated design. A common denominator for previously constructed local hybrid funtionals is usage of thermochemical benchmark data to construct these functionals. Herein, we design a
local hybrid functional without relying on benchmark data. Instead, we construct it in a more ab initio manner, following the principles of modern meta-generalized gradient approximations and considering theoretical constrains. To achieve this, we make use of the density matrix expansion and a local mixing function based on an approximate correlation length. The accuracy of the developed density functional approximation is assessed for thermochemistry, excitation energies, polarizabilities, magnetizabilities, NMR spin–spin coupling constants, NMR shieldings and shifts, as well as EPR g-tensors and hyperfine coupling constants. Here, the new exchange functional shows a robust performance and is especially well suited for atomization energies, barrier heights, excitation energies, NMR coupling constants, and EPR properties, whereas it looses some ground for the NMR shifts. Therefore, the designed functional is a major step forwards for functionals that have been designed from first principles. | Christof Holzer; Yannick J. Franzke | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628b860770876776975c9e43/original/a-local-hybrid-exchange-functional-approximation-from-first-principles.pdf |
6758719d7be152b1d08918d3 | 10.26434/chemrxiv-2024-vcdxr | NMR characterization of the diastereomeric composition of a model therapeutic oligonucleotide | There is an increasing demand from the pharmaceutical industry and regulatory agencies for analytical methods capable of accurately characterizing therapeutic oligonucleotides (ONs). In this work, we present the full NMR characterization of a model therapeutic ON (mtON) containing eight chemically modified nucleotide units and a phosphorothioate (PS) internucleotide linkage at each of its two extremities. Because of the presence of two P-chiral PS linkages and the lack of stereocontrol during conventional solid-phase synthesis, our 8-mer ON consists of a mixture of four diastereomers. NMR spectra acquired at 1 GHz and 600 MHz allowed the full assignment of the 1H, 13C, 31P and 19F signals of mtON, the confirmation of its primary structure, as well as the identification, and quantification of all the diastereomers. | Bartomeu Mir; Margarida Gairí; M. Teresa González; Ariadna Vila-Planas; Maksim Mayzel; Miquel Pons; Martial Piotto; Montserrat Terrazas | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6758719d7be152b1d08918d3/original/nmr-characterization-of-the-diastereomeric-composition-of-a-model-therapeutic-oligonucleotide.pdf |
64d4cfca4a3f7d0c0defb22e | 10.26434/chemrxiv-2023-3jczj | Molecular rhodium complex within N-rich porous polymer macroligand as heterogeneous catalyst for the visible-light driven CO2 photoreduction | The heterogenization of molecular catalysts within a porous solid acting as macroligand can advantageously open access to enhanced stability and productivity, and thus to more sustainable catalytic process. We report here porous organic polymer (POP) made through metal-free polymerization using bipyridine repeating units. This N-rich POP is an efficient macroligand for the heterogenization of molecular rhodium complexes. The intrinsic catalytic activity of the heterogenized catalyst is slightly higher than that of its homogeneous molecular counterpart for formic acid production as unique carbon containing product. The heterogenization of the rhodium catalysts enables recycling for a total productivity up to 8.3 grams of formic acid per gram of catalyst after 7 cycles of reaction using visible light as sole energy source. | Rajashree Newar; Ashta C. Ghosh; Remy Rajapaksha; Partha Samanta; Florian M. Wisser; Jerome Canivet | Materials Science; Catalysis; Energy; Catalysts; Heterogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d4cfca4a3f7d0c0defb22e/original/molecular-rhodium-complex-within-n-rich-porous-polymer-macroligand-as-heterogeneous-catalyst-for-the-visible-light-driven-co2-photoreduction.pdf |
63f376899da0bc6b333f8612 | 10.26434/chemrxiv-2023-2v4cx-v2 | Fractional-Electron and Transition-Potential Methods for Core-to-Valence Excitation Energies Using Density Functional Theory | Methods for computing x-ray absorption spectroscopy at the self-consistent field level are examined, based on a constrained core hole (possibly containing a fractional electron), and in some cases promoting an electron or a fraction of an electron into the virtual space. These methods are based on Slater's transition concept and its generalizations (including the transition-potential method), wherein core-to-valence excitation energies are determined using Kohn-Sham orbital energies. Variants of this idea are systematically tested, revealing a best-case accuracy of 0.3-0.4 eV with respect to experiment for K-edge excitation energies, although errors are much larger in many cases. For higher-lying near-edge transitions, even the best of these methods affords errors of ~2 eV. Absolute errors are reduced below 1 eV by introducing an empirical shift based on a charge-neutral transition-potential method, in conjunction with functionals such as SCAN, SCAN0, or B3LYP. This procedure affords an entire excitation spectrum from a single fractional-electron calculation, at the cost of ground-state density functional theory and without the need for state-by-state calculations. This shifted transition-potential approach may be especially useful for simulating transient spectroscopies or in complex systems where excited-state Kohn-Sham calculations are challenging, | Subrata Jana; John Herbert | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f376899da0bc6b333f8612/original/fractional-electron-and-transition-potential-methods-for-core-to-valence-excitation-energies-using-density-functional-theory.pdf |
60c750a7842e65efc2db3a66 | 10.26434/chemrxiv.13066082.v1 | Structure Revision of Protoaculeine B, a Posttranslationally Modified N-Terminal Residue in the Peptide Toxin Aculeine B | <div>Here, we newly propose the structure of protoaculeine B, an N-terminal moiety of the marine peptide toxin aculeine B, as possessing the cis-disubstituted tetrahydro-beta-carboline framework. We prepared two truncated model compounds that lack long-chain polyamine by one-step Pictet-Spengler reaction of tryptophan, and compared the NMR and mass spectra and chemical reactivity with those of natural protoaculeine B. The synthetic models reproduced the profiles of the natural product well, which was conclusive for the structural revision.</div> | Raku Irie; Kei Miyako; Satoko Matsunaga; Ryuichi Sakai; Masato Oikawa | Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750a7842e65efc2db3a66/original/structure-revision-of-protoaculeine-b-a-posttranslationally-modified-n-terminal-residue-in-the-peptide-toxin-aculeine-b.pdf |
6317e24e3e2e3657d92d3e00 | 10.26434/chemrxiv-2022-49tzw | Ritonavir Form III: Lightning strikes twice at the same time, 137 miles apart | Polymorph screening is a crucial step in the characterization and development of pharmaceuticals. The 1998 recall of ritonavir upon the unexpected appearance of the more stable Form II polymorph remains a notorious case of disappearing polymorphs as the presence of Form II inhibited the ability to grow the original Form I. This study presents the characterization of Form III of ritonavir grown from melt/cool crystallization. While Form III has been observed by researchers in 2014 and 2022, this study presents a thorough characterization and novel thermal profile for quicker nucleation and crystallization of the new form. In this work, we expand upon past thermal methods examining the polymorphic landscape of ritonavir to shed light on the crystallization of Form III from the melt. | Stephan Parent; Pamela Smith; Dale Purcell; Daniel Smith; Susan Bogdanowich-Knipp; Ami Bhavsar; Larry Chan; Jordan Croom; Haley Bauser; Andrew McCalip; Stephen Byrn; Adrian Radocea | Physical Chemistry; Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6317e24e3e2e3657d92d3e00/original/ritonavir-form-iii-lightning-strikes-twice-at-the-same-time-137-miles-apart.pdf |
60c75945842e650ceddb49d7 | 10.26434/chemrxiv.14676528.v1 | Enantioselective a,d-Difunctionalization of Dienes Initiated by Rh-Catalyzed Conjugate Addition | Metal-catalyzed enantioselective conjugate additions are highly reliable methods for stereoselective synthesis, however multi-component reactions that are initiated by conjugate arylation of acyclic p-systems are rare. These processes generally proceed with poor diastereoselectivity while requiring basic, moisture sensitive organometallic nucleophiles. Here we show that Rh-catalysts supported by a tetrafluorobenzobarrelene ligand (Ph-tfb) enable the enantio-, diastereo-, and Z-selective a,d-difunctionalization of electron-deficient 1,3-dienes with organoboronic acid nucleophiles and aldehyde electrophiles to generate Z-homoallylic alcohols with three stereocenters. The reaction accommodates diene substrates activated by ester, amide, ketone, or aromatic groups and can be used to couple aryl, alkenyl, or alkyl aldehydes. Diastereoselective functionalization of the Z-olefin unit in the addition products allow for the generation of compounds with five stereocenters in high dr and ee. Mechanistic studies suggest aldehyde allylrhodation is the rate determining step, and unlike reactions of analogous Rh-enolates, the Rh-allyl species generated by d-arylation undergoes aldehyde trapping rather than protonolysis, even when water is present as a co-solvent. These findings should have broader implications in the use of privileged metal-catalyzed conjugate addition reactions as entry points towards the preparation of acyclic molecules containing non-adjacent stereocenters. | Christopher Cooze; Wesley McNutt; Markus Schoetz; Bohdan Sosunovych; Svetlana Grigoryan; Rylan Lundgren | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75945842e650ceddb49d7/original/enantioselective-a-d-difunctionalization-of-dienes-initiated-by-rh-catalyzed-conjugate-addition.pdf |
6644b47291aefa6ce111a27a | 10.26434/chemrxiv-2024-mpztp | A spectroscopic and computational evaluation of uranyl oxo engagement with transition metal cations | We report the synthesis and characterization of five novel Cd2+/UO¬22+ heterometallic complexes that feature Cd-oxo distances ranging from 78% to 171% of the sum of the van der Waals radii for these atoms. This work marks an extension of our previously reported Pb2+/UO22+ and Ag+/UO22+ complexes, yet with much more pronounced structural and spectroscopic effects resulting from Cd-oxo interactions. We observe a major shift in the U=O symmetric stretch and significant uranyl bond length asymmetry. The ρbcp¬ values calculated using Quantum Theory of Atoms in Molecules (QTAIM) support the asymmetry displayed in the structural data and indicate a decrease in covalent character in U=O bonds with close Cd-oxo contacts; more so than in related compounds containing Pb2+ and Ag+. Second Order Perturbation Theory (SOPT) analysis reveals that O spx Cd s is the most significant orbital overlap and U=O bonding and antibonding orbitals also contribute to the interaction (U=O σ/π Cd d and Cd s U=O σ/π*). The overall stabilization energies for these interactions were lower than those in previously reported Pb2+ cations, yet larger than related Ag+ compounds. Analysis of the equatorial coordination sphere of the Cd2+/UO¬22+ compounds (along with Pb2+/UO¬22+ complexes) reveals that 7-coodinate uranium favors closer, stronger Mn+-oxo contacts. These results indicate that U=O bond strength tuning is possible with judicious choice of metal cations for oxo interactions and equatorial ligand coordination. | Dominique Brager; Ahan Panchal; Christopher Cahill | Theoretical and Computational Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Spectroscopy (Inorg.); Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6644b47291aefa6ce111a27a/original/a-spectroscopic-and-computational-evaluation-of-uranyl-oxo-engagement-with-transition-metal-cations.pdf |
64f66b6add1a73847f33c314 | 10.26434/chemrxiv-2023-pcx2m | Mechanisms of Highly Efficient Photocatalytic Pollutant Degradation by Au/TiO2 Janus Nanoparticles | Semiconductor nanoparticles partially coated with metals have been widely used to degrade contaminants in water, but the physical mechanisms underlying degradation are poorly understood, limiting their real-world implementation. Here, we reveal the degradation mechanisms that dominate when gold-coated titanium dioxide (Au/TiO2) “Janus” nanoparticles (JNPs) are irradiated with monochromatic ultraviolet light (254 nm and 365 nm wavelengths) to degrade 1,4-dioxane, a carcinogenic model pollutant. To do so, we performed experiments with ultraviolet light at different wavelengths with and without radical quenching, extensive JNP characterization (SEM, XRD, EDS, DLS, and UV-Vis), and 3D simulations of self-propulsion and light-matter interactions. We traced the enhanced photocatalytic activity of Au-coated JNPs to both increased light absorption due to Au acting as an optical antenna, and inhibited recombination of photogenerated electrons and holes. These two effects increase the production of hydroxyl radicals, accelerating the degradation of 1,4-dioxane. The reduced electron/hole recombination is due to two factors: the Schottky barrier that forms between Au and TiO2 (which drives photogenerated electrons from TiO2 into the metal), and stoichiometric changes in the TiO2 that accompany gold sputtering which facilitate electron sequestration by the metal. In contrast, self-propulsion and surface plasmon resonance play at most a minor role. | Matthew Tao; Yangyuan Ji; Lamar Mair; Yuhang Fang; Amit Singh; Thomas Beechem; David Warsinger; Jeffrey Moran | Catalysis; Nanoscience; Earth, Space, and Environmental Chemistry; Wastes; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f66b6add1a73847f33c314/original/mechanisms-of-highly-efficient-photocatalytic-pollutant-degradation-by-au-ti-o2-janus-nanoparticles.pdf |
64590e461ca6101a45fe66b9 | 10.26434/chemrxiv-2023-dd1hc-v2 | Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations | Alchemical absolute binding free energy calculations are of increasing interest in drug discovery. These calculations require restraints between the receptor and ligand to restrict their relative positions and, optionally, orientations. Boresch restraints are commonly used, but they must be carefully selected in order to sufficiently restrain the ligand and to avoid inherent instabilities. Applying multiple distance restraints between anchor points in the receptor and ligand provides an alternative framework without inherent instabilities which may provide convergence benefits by more strongly restricting the relative movements of the receptor and ligand. However, there is no simple method to calculate the free energy of releasing these restraints due to the coupling of the internal and external degrees of freedom of the receptor and ligand. Here, a method to rigorously calculate free energies of binding with multiple distance restraints by imposing intramolecular restraints on the anchor points is proposed. Ab- solute binding free energies for the human macrophage migration inhibitory factor - MIF180 system obtained using a variety of Boresch restraints and rigorous and non- rigorous implementations of multiple distance restraints are compared. It is shown that several multiple distance restraints schemes produce estimates in good agreement with Boresch restraints. In contrast, calculations without orientational restraints produce erroneously favourable free energies of binding by up to approximately 4 kcal mol−1. These approaches offer new options for the deployment of alchemical absolute binding free energy calculations. | Finlay Clark; Graeme Robb; Daniel Cole; Julien Michel | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64590e461ca6101a45fe66b9/original/comparison-of-receptor-ligand-restraint-schemes-for-alchemical-absolute-binding-free-energy-calculations.pdf |
61c09caaf52bc47a2dc756d7 | 10.26434/chemrxiv-2021-6kzlt | Interdependent Dynamic Nitroaldol and Boronic Ester Reactions for Complex Dynamers of Different Topologies | Complex dynamic systems displaying interdependency between nitroaldol and boronic ester reactions have been demonstrated. Nitroalkane-1,3-diols, generated by the nitroaldol reaction, were susceptible to ester formation with different boronic acids in aprotic solvents, whereas hydrolysis of the esters occurred in the presence of water. The boronic ester formation led to significant stabilization of the nitroaldol adducts under basic conditions. The use of bifunctional building blocks was furthermore established, allowing for main chain nitroaldol-boronate dynamers as well as complex network dynamers with distinct topologies. The shape and rigidity of the resulting dynamers showed an apparent dependency on the configuration of the boronic acids. | Antanas Karalius; Yunchuan Qi; Mubarak Ayinla; Zoltan Szabo; Olof Ramstrom | Organic Chemistry; Materials Science; Polymer Science; Supramolecular Chemistry (Org.); Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c09caaf52bc47a2dc756d7/original/interdependent-dynamic-nitroaldol-and-boronic-ester-reactions-for-complex-dynamers-of-different-topologies.pdf |
6448fd24e4bbbe4bbf475860 | 10.26434/chemrxiv-2023-h1gqd | GUIDEMOL: a Python graphical user interface for molecular descriptors based on RDKit | GUIDEMOL is a Python computer program based on the RDKit software to process molecular structures and calculate molecular descriptors with a graphical user interface using the tkinter package. It can calculate descriptors already implemented in RDKit as well as grid representations of 3D molecular structures using the electrostatic potential or voxels. The GUIDEMOL app provides an easy access to RDKit tools for chemoinformatics users with no programming skills and can be adapted to calculate other descriptors or to trigger other procedures. A CLI is also provided for the calculation of grid representations. The source code is available at https://github.com/jairesdesousa/guidemol | Joao Aires-de-Sousa | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6448fd24e4bbbe4bbf475860/original/guidemol-a-python-graphical-user-interface-for-molecular-descriptors-based-on-rd-kit.pdf |
642ec95fa41dec1a5695b20a | 10.26434/chemrxiv-2023-8f0lk | Polymer Architecture Alters Tissue Distribution and Enhances Cytotoxicity Profiles in Orthotopic Models of Triple Negative Breast Cancers | The efficacy of nanomedicines is dependent on their access to target sites in the body, and this in turn is affected by their size, shape and transport properties in tissue. Although there have been many studies, the ability to design nanomaterials with optimal physicochemical properties for in vivo efficacy remains a significant challenge. In particular, it is difficult to quantify the detailed effects of cancer drug delivery systems in vivo as tumour volume reduction, a commonly reported marker of efficacy, does not always correlate with cytotoxicity in tumour tissue. Here, we studied the behaviour in vivo of two specific poly(2-hydroxypropyl methacrylamide) (pHPMA) pro-drugs, with the same chemical compositions of redox-responsive backbone components and pH-sensitive linkers to the anti-cancer drug doxorubicin but with varying architectures, in this case hyperbranched and star-shaped. Evaluation of the biodistribution of these polymers following systemic injection indicated differences in the circulation time and organ distribution of the two polymers, despite their very similar hydrodynamic radii (~ 10 and 15 nm) and underlying chemistry of backbone, side-chain and pro-drug linkers. In addition, both polymers showed improved tumour accumulation in orthotopic triple-negative breast cancers in mice, and decreased accumulation in healthy tissue, as compared to free doxorubicin. Importantly, there was a significant increase in tumour accumulation for the hyper-branched polymer compared to the star polymer, suggesting a possible role for solution conformations of these materials, rather than the chemistries, in mediating their performance. The results of haematoxylin and eosin assays, and TUNEL staining indicated a higher population of apoptotic cells in the tumours for both polymer pro-drug treatments, and in turn a lower population of apoptotic cells in the heart, liver and spleen, as compared to free doxorubicin. In particular, the hyperbranched polymer demonstrated significantly higher tumour deposition and apoptosis levels than its star shaped counterpart. Taken together, these data suggest that the penetration of both of these polymer pro-drugs was enhanced in tumour tissue relative to free doxorubicin, and that the combination of size, architecture, bioresponsive backbone and drug linker degradation yielded greater efficacy for the polymers as measured by biomarkers other than that of tumour volume. | Cara Moloney; Fatemeh Mehradnia; Robert J Cavanagh; Asmaa Ibrahim; Amanda K Pearce; Alison Ritchie; Philip Clarke; Ruman Rahman; Anna Grabowska; Cameron Alexander | Materials Science; Polymer Science; Biocompatible Materials; Controlled-Release Systems; Drug delivery systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642ec95fa41dec1a5695b20a/original/polymer-architecture-alters-tissue-distribution-and-enhances-cytotoxicity-profiles-in-orthotopic-models-of-triple-negative-breast-cancers.pdf |
60c73f9d702a9ba109189f33 | 10.26434/chemrxiv.7439159.v1 | Valence: A Massively Parallel Implementation of the Variational Subspace Valence Bond Method | This work describes the software package, Valence, for the calculation of molecular<br />energies using the variational subspace valence bond (VSVB) method. VSVB is a highly scalable ab initio electronic structure method based on non-orthogonal orbitals. Important features of practical value include: Valence bond wave functions of Hartree–Fock quality can be constructed with a single determinant; excited states can be modeled with a single configuration or determinant; wave functions can be constructed automatically by combining orbitals from previous calculations. The opensource software package includes tools to generate wave functions, a database of generic orbitals, example input files, and a library build intended for integration with other packages. We also describe the interface to an external software package, enabling the computation of optimized molecular geometries and vibrational frequencies. | Graham Fletcher; Colleen Bertoni; Murat Keçeli; Michael D'Mello | Bonding; Computational Chemistry and Modeling; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9d702a9ba109189f33/original/valence-a-massively-parallel-implementation-of-the-variational-subspace-valence-bond-method.pdf |
6758c63c7be152b1d08fa37b | 10.26434/chemrxiv-2024-n3np0 | Size-dependent effects of Ge addition on the coking and sintering tendency of PtnGex/alumina
(n=4,7,11) model catalysts | The reactivity and adsorbate binding properties of alumina-supported Ptn and PtnGem (n/m = 4/1,
7/2, 11/4) model catalysts were studied using a combination of ethylene and CO temperatureprogrammed
desorption (TPD), He+ ion scattering (ISS), and detailed density functional theory
(DFT). The Ptn/alumina catalysts gradually deactivated in repeated CO TPD runs and deactivated
more rapidly in repeated ethylene TPD runs due to the effects of sintering and carbon deposition
(coking). PtnGem/alumina catalysts were dramatically more stable against deactivation by both
sintering and coking. Carbon addition to Ptn/alumina also increased stability against sintering, but not
coking. Ion scattering was used to probe the nature of adsorbate binding, including the effects of both
carbon and Ge addition on the accessibility of strong Pt-associated binding sites for ethylene and CO.
DFT was used to examine the electronic and geometric structures and ethylene and CO binding
properties of Ptn (n = 4, 7) with added Ge, carbon, or both. Consistent with the ISS results, DFT
shows that loss of strong adsorbate binding sites mostly resulted from changes to the electronic
properties of the clusters, rather than simple blocking of binding sites by Ge or carbon | Guangjing Li; Shawn Chiu; Harry Morgan; Autumn Fuchs; Avital Isakov; Patricia Poths; Zisheng Zhang; Anastassia Alexandrova; Scott Anderson | Physical Chemistry; Catalysis; Nanoscience; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Clusters | CC BY 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6758c63c7be152b1d08fa37b/original/size-dependent-effects-of-ge-addition-on-the-coking-and-sintering-tendency-of-ptn-gex-alumina-n-4-7-11-model-catalysts.pdf |
66b0ed9401103d79c5ce5e8c | 10.26434/chemrxiv-2024-r9gm2-v2 | Automation in Electrifying Flow Organic Synthesis | Organic electrochemical synthesis may be combined with continuous flow and automation technology. Here, the authors highlight the benefits if such chemical engineering approaches along with technology and software directions taking organic chemistry into the future. | Tomas Hardwick; Nisar Ahmed | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b0ed9401103d79c5ce5e8c/original/automation-in-electrifying-flow-organic-synthesis.pdf |
60c74808337d6c357ce2747e | 10.26434/chemrxiv.11841141.v1 | Direct Arsenic Removal from Water Using Non-Membrane, Low Temperature Directional Solvent Extraction | Arsenic (<i>As</i>)
poisoning in water due to natural minerals or industrial pollution is a
critical global problem that threatens the health and life of billions. Current
arsenic removal techniques involving chemical reaction, ion exchange, or
membrane processes can be expensive, inaccessible or infeasible for
underdeveloped regions or remote areas. Here, we demonstrate that using a so-called
directional solvent extraction (DSE) process, arsenic<i> </i>ions in water can be effectively removed without the need of a membrane
or chemical reaction, and this process promises to utilize very low temperature
heat (as low as 45 <sup>o</sup>C). We have tested feed water with different arsenic
concentrations and arsenic ions in different forms (<i>As</i>-III and <i>As</i>-V) commonly
found in nature. It is demonstrated that DSE using decanoic acid as the
directional solvent can purify contaminated water to meet the drinking water
standard (arsenic concentration < 10 parts per billion, ppb), and the
arsenic removal efficiencies are higher than 91% for <i>As</i>-III and 97% for <i>As</i>-V.
Moreover, DSE can remove <i>As</i>-III
directly without the need of pre-oxidation, which is required in most of the
state of art techniques. DSE can potentially lead to effective arsenic removal
technologies with low resource settings that are suitable for remote and underdeveloped
regions, which are impacted by arsenic poisoning the most. | Jiaji Guo; Shirui Luo; Zeyu Liu; Tengfei Luo | Environmental Science; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74808337d6c357ce2747e/original/direct-arsenic-removal-from-water-using-non-membrane-low-temperature-directional-solvent-extraction.pdf |
657c85f7e9ebbb4db9f7e2df | 10.26434/chemrxiv-2023-p59c1 | Pyrylium- and pyridinum-based ionic liquids as friction modifiers for greases | The use of ionic liquids as lubricants or lubricant additives has been studied extensively over the past few decades. However, the ionic liquids considered for lubricant applications thus far have been part of a limited structural class of phosphonium- or imidazolium-type compounds. Here, new pyrylium- and pyridinium-based ionic liquids bearing long alkyl chains were prepared and evaluated as friction and wear-reducing additives in naphthenic greases. The physical properties of the synthetic ionic liquids and additized-naphthenic grease were measured. The tribological performance of the greases was measured using standard benchtop tests and shown, in some cases, to decrease friction compared to the base grease. The compatibility of the synthetic ionic liquids with the naphthenic greases is tentatively proposed to be a result of molecular structure and its potential influence on miscibility and tribological performance. | Miguel Chacon Teran; Cinderella Moustafa; Joanne Luu; Ashlie Martini; Michael Findlater | Organic Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Organic Compounds and Functional Groups; Fuels - Materials; Fluid Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657c85f7e9ebbb4db9f7e2df/original/pyrylium-and-pyridinum-based-ionic-liquids-as-friction-modifiers-for-greases.pdf |
6710c55312ff75c3a1ad3b8f | 10.26434/chemrxiv-2024-36l28 | ML- Accelerated Automatic Process Exploration Reveals Facile O-Induced Pd Step-Edge Restructuring on Catalytic Time Scales | We combine automatic process exploration with an iteratively trained machine- learning interatomic potential to systematically identify elementary processes occur- ring during the initial oxidation of a Pd step edge. Corresponding process lists are a prerequisite to overcome prevalent predictive-quality microkinetic modeling approaches which consider only a minimum number of hand-selected and thus typically intuitive processes. The exploration readily generates close to 3000 inequivalent elementary processes and thus unveils a complexity far beyond current microkinetic modeling ca- pabilities. Among these processes are numerous low-barrier processes involving the col- lective motion of several atoms that enable a facile O-mediated restructuring of the Pd step edge through the motion of larger PdxOy units. The concomitant interconversion happens on time scales comparable to those of molecular processes of heterogeneous oxidation catalysis. This suggests a dynamic aspect of the operando evolution of the working interface reminiscent of the fluxionality discussed in nanocluster catalysis. | Patricia Poths; King Chun Lai; Francesco Cannizzaro; Christoph Scheurer; Sebastian Matera; Karsten Reuter | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Nanocatalysis - Reactions & Mechanisms | CC BY 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710c55312ff75c3a1ad3b8f/original/ml-accelerated-automatic-process-exploration-reveals-facile-o-induced-pd-step-edge-restructuring-on-catalytic-time-scales.pdf |
65ffbfe79138d2316129b0df | 10.26434/chemrxiv-2024-fl4x3 | Differing Plasmonic Intra-nanoparticle and Inter-nanoparticle Molecular Reaction Rates at the Three-Phase Contact Line of an Evaporating Sessile Droplet | Intra-nanoparticle and inter-nanoparticle heterogeneous chemical reaction pathways may involve different kinetic, dynamic natures and product selectivity like intramolecular and intermolecular counterparts in chemical synthesis and may involve rich chemistry. However, that is yet to be demonstrated. Herein, we utilized the phase change behavior of silver nanoparticles (AgNPs) from dispersion to deposition at the three-phase contact line (TPCL) in evaporating aqueous (H2O/D2O) droplet to experimentally monitor the plasmonic dimerization of 4-aminothiophenol (4-ATP) to 4,4´-dimercaptoazobenzene (DMAB) by surface-enhanced Raman spectroscopy (SERS). Raman signature of the solvent attached probe molecules in conjugation with density functional theory (DFT) calculations and DMAB formation in two steps suggested sequential intraparticle and interparticle DMAB formation, the former being ~3 times and ~1.5 times faster than the later in H2O and D2O, respectively. | SUJAY PAUL; ARUN CHATTOPADHYAY | Physical Chemistry; Catalysis; Nanoscience; Plasmonic and Photonic Structures and Devices; Heterogeneous Catalysis; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ffbfe79138d2316129b0df/original/differing-plasmonic-intra-nanoparticle-and-inter-nanoparticle-molecular-reaction-rates-at-the-three-phase-contact-line-of-an-evaporating-sessile-droplet.pdf |
67277b835a82cea2fae58c11 | 10.26434/chemrxiv-2024-g3r93 | Data-Driven Improvement of Local Hybrid Functionals: Neural-Network-Based Local Mixing Functions and Power-Series Correlation Functionals | Local hybrid functionals (LHs) are a modern class of density functionals that use a real-space position-dependent admixture of exact exchange (EXX), governed by a local mixing function (LMF). While many model LMFs have been proposed and evaluated over the past 10-20 years, their systematic construction has been hampered by a lack of exact physical constraints on their valence behavior. Here we exploit a data-driven approach and train a new type of "n-LMF" as a relatively shallow neural network. The input features of this n-LMF are of meta-GGA character, while the W4-17 atomization-energy and BH76 reaction-barrier test sets have been used for training. Simply replacing the widely used "t-LMF" of the LH20t functional by the n-LMF provides the LH24n-B95 functional. Augmented by DFT-D4 dispersion corrections, LH24n-B95-D4 remarkably improves the WTMAD-2 value for the large GMTKN55 test suite of general main-group thermochemistry, kinetics and noncovalent interactions (NCIs) from 4.55 kcal/mol to 3.49 kcal/mol. As we found the limited flexibility of the B95c correlation functional to disfavor much further improvement on NCIs, we proceeded to replace it by an optimized B97c-type power-series expansion. This gives the LH24n functional. LH24n-D4 gives a WTMAD-2 value of 3.10 kcal/mol, the so far lowest value of a rung 4 functional in self-consistent calculations. The new functionals perform moderately well for organometallic transition-metal energetics while leaving room for further data-driven improvements in that area. Compared to complete neural-network functionals like DM21, the present more tailored approach to train just the LMF in a flexible but well-defined human-designed LH functional retains the possibility of graphical LMF analyses to gain deeper understanding. We find that both the present n-LMF and the recent x-LMF suppress the so-called gauge problem of local hybrids without adding a calibration function as required for other LMFs like the t-LMF. LMF plots show that this can be traced back to large LMF values in the small-density region between the interacting atoms in NCIs for n- and x-LMFs and low values for the t-LMF. We also find that the trained n-LMF has relatively large values in covalent bonds without deteriorating binding energies. The current approach enables fast and efficient routine self-consistent calculations using n-LMFs in Turbomole. Further routes toward improved functionals are delineated. | Artur Wodyński; Kilian Glodny; Martin Kaupp | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67277b835a82cea2fae58c11/original/data-driven-improvement-of-local-hybrid-functionals-neural-network-based-local-mixing-functions-and-power-series-correlation-functionals.pdf |
60c74087567dfe6146ec3bb5 | 10.26434/chemrxiv.7761791.v1 | The Different Organization of Water in Zeolite L and Its MOF Mimic | Abstract:<div>Confinement of molecules inside one dimensional arrays of
channel-shaped cavities has led to an impressive number of
technologically interesting materials. However, the
interactions governing the properties of the supramolecular
aggregates still remain obscure, even in the case of the most
common guest molecule: water. Herein, we use
computational chemistry methods (#compchem) to study
the water organization inside two different channel-type
environments: zeolite L – a widely used matrix for
inclusion of dye molecules, and ZLMOF – the closest
metal-organic-framework mimic of zeolite L. In ZLMOF,
the methyl groups of the ligands protrude inside the
channels, creating nearly isolated nanocavities. These
cavities host well-separated ring-shaped clusters of water
molecules, dominated mainly by water-water hydrogen
bonds. ZLMOF channels thus provide arrays of „isolated
supramolecule“ environments, which might be exploited for
the individual confinement of small species with interesting
optical or catalytic properties. In contrast, the one
dimensional nanochannels of zeolite L contain a continuous
supramolecular structure, governed by the water
interactions with potassium cations and by water-water
hydrogen bonds. Water molecules impart a significant
energetic stabilization to both materials, which increases by
increasing the water content in ZLMOF, while the opposite
trend is observed in zeolite L. The water network in zeolite
L contains an intriguing hyper-coordinated structure, where
a water molecule is surrounded by 5 strong hydrogen
bonds. Such a structure, here described for the first time in
zeolites, can be considered as a water pre-dissociation
complex and might explain the experimentally detected
high proton activity in zeolite L nanochannels. </div> | gloria tabacchi; Ettore Fois | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Self-Assembly; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74087567dfe6146ec3bb5/original/the-different-organization-of-water-in-zeolite-l-and-its-mof-mimic.pdf |
60c73f969abda27b67f8baff | 10.26434/chemrxiv.7399532.v1 | Synthesis and Structures of Stable Pt(II) and (IV) Alkylidenes: Evidence for π-Bonding and Relativistic Stabilization | Isolable
cationic Pt(II) and Pt(IV) alkylidenes, proposed intermediates in catalytic
organic transformations, are reported. The bonding in these species was probed
by experimental, structural, spectroscopic, electrochemical and computational
methods, providing direct evidence for π-bonding, the oft-theorized
relativistic stabilisation of these species, and the influence of oxidation
state. | Etienne A. LaPierre; Warren Piers; Jian-Bin Li; Chris Gendy | Bonding; Electrochemistry; Organometallic Compounds; Reaction (Inorg.); Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f969abda27b67f8baff/original/synthesis-and-structures-of-stable-pt-ii-and-iv-alkylidenes-evidence-for-bonding-and-relativistic-stabilization.pdf |
60c74789702a9bc31c18add8 | 10.26434/chemrxiv.11709057.v1 | Accessing the Two-Electron Charge Storage Capacity of MnO2 in Mild Aqueous Electrolytes | <p>Rechargeable batteries based on MnO2 cathodes, able to operate in mild aqueous electrolytes, have attracted remarkable attention due to their appealing features for the design of low-cost stationary energy storage devices. However, the charge/discharge mechanism of MnO2 in such media is still unclear and a matter of debate. Here, an in-depth quantitative spectroelectrochemical analysis of MnO2 thin-films provides a set of important new mechanistic insights. A major finding is that charge storage occurs through the reversible two electron faradaic conversion of MnO2 into water-soluble Mn2+ in the presence of a wide range of weak Brønsted acids, including the [Zn(H2O)6]2+ or [Mn(H2O)6]2+ complexes commonly present in aqueous Zn/MnO2 batteries. Furthermore, it is evidenced that buffered electrolytes loaded with Mn2+ are ideal to achieve highly reversible conversion of MnO2 with both high gravimetric capacity and remarkably stable charging/discharging potentials. In the most favorable case, a record gravimetric capacity of 450 mA·h·g-1 was obtained at a high rate of 1.6 A·g-1, with a coulombic efficiency close to 100% and a MnO2 utilization of 84%. Overall, the present results challenge the common view on MnO2 charge storage mechanism in mild aqueous electrolytes and underline the benefit of buffered electrolytes for high-performance rechargeable aqueous batteries.<br /></p> | Mickaël Mateos; Nikolina Makivic; Yee-Seul Kim; Benoit Limoges; Véronique Balland | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74789702a9bc31c18add8/original/accessing-the-two-electron-charge-storage-capacity-of-mn-o2-in-mild-aqueous-electrolytes.pdf |
635b946e55a0810ba7c8d212 | 10.26434/chemrxiv-2022-2ktc5-v2 | An Image Based 3D Modelling Framework for Li-S Batteries | Traditionally, 1D volume-averaged continuum approaches are used to model Li-S battery performance at varying C-rates. For the first time, we present a working three-dimensional electrochemical model of a Li-S battery based on real electrode microstructure. In this study we evaluate the gaps between a volume-averaged 1D electrochemical model and a microstructurally resolved 3D image-based electrochemical model to accurately predict the effects of the localised heterogeneities present in Li-S cathodes on the battery performance at varying C-rates. The real microstructure of the commercial electrode was obtained using micro–X-ray computed tomography and used as a framework for an image-based 3D electrochemical model of the Li-S battery. The extent of heterogeneities present in the electrode architecture and the adequacy of using the representative elementary volume to capture the effect of complex electrode microstructure on the cell performance were analysed by mapping the 3D electrode microstructure. In this study, three-dimensional, microstructurally-resolved, image-based electrochemical models were developed on sub-volumes of the electrode to evaluate the effect of heterogeneous structure on the localised performance, which are further compared with the 1D model developed using the volume-averaged effective microstructural properties obtained from the X-ray CT image. Finally, the future modelling framework that would aid in optimising the S/C structure for improved and uniform cell performance is discussed. | Xiaoyu Dai; Nivedita Kulkarni; James B. Robinson; Dan J.L. Brett; Paul R. Shearing; Rhodri Jervis | Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635b946e55a0810ba7c8d212/original/an-image-based-3d-modelling-framework-for-li-s-batteries.pdf |
60c73eda469df4d712f42960 | 10.26434/chemrxiv.7130852.v1 | A Biocatalytic Platform for Synthesis of Chiral α-Trifluoromethylated Organoborons | <p></p><p>There are few biocatalytic transformations that produce fluorine-containing molecules prevalent in modern
pharmaceuticals. To expand the scope of biocatalysis for organofluorine
synthesis, we have developed an enzymatic platform for highly enantioselective
carbene B–H bond insertion to yield
versatile <i>α-</i>trifluoromethylated (<i>α</i>-CF<sub>3</sub>) organoborons, an important class of
organofluorine molecules that contain stereogenic centers bearing both CF<sub>3</sub> and
boron groups. In contrast to current
‘carbene transferase’ enzymes that use a limited set of simple diazo compounds
as carbene precursors, this system based on <i>Rhodothermus
marinus</i> cytochrome <i>c</i> (<i>Rma</i> cyt <i>c</i>) can accept a broad range of
trifluorodiazo alkanes and deliver versatile chiral <i>α</i>-CF<sub>3</sub> organoborons with total turnovers up to 2870 and
enantiomeric ratios up to 98.5:1.5. Computational modeling reveals that this
broad diazo scope is enabled by an active site environment that directs the
alkyl substituent on the heme CF<sub>3</sub>-carbene intermediate towards the
solvent-exposed face, thereby allowing the protein to accommodate diazo
compounds with diverse structural features.</p><br /><p></p> | Xiongyi Huang; Marc Garcia-Borràs; Kun Miao; S. B. Jennifer Kan; Arjun Zutshi; K. N. Houk; Frances H. Arnold | Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73eda469df4d712f42960/original/a-biocatalytic-platform-for-synthesis-of-chiral-trifluoromethylated-organoborons.pdf |
65dd159966c1381729a09837 | 10.26434/chemrxiv-2023-p0f1s-v2 | Comments on “Does φ-Aromaticity exist in prismatic {Bi6}-based clusters?” | We read the manuscript by Dariusz W. Szczepanik and Miquel Solà with interest, and recognized several misinterpretations (based on oversimplifications) of our work and also errors that results from inappropriate/insufficient methods applied in their follow-up studies. This led to erroneous statements, which the authors additionally mixed with statements on aromaticity, which does not fully comply with definitions that have been well-established, e.g., for benzene. In this comment, we outline the misinterpretations, errors, and questionable statements, thereby referring to our work and further literature to underline the facts. | Benjamin Peerless; Andreas Schmidt; Yannick J. Franzke; Stefanie Dehnen | Theoretical and Computational Chemistry; Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dd159966c1381729a09837/original/comments-on-does-aromaticity-exist-in-prismatic-bi6-based-clusters.pdf |
63081623eadd9a7fa381c0a2 | 10.26434/chemrxiv-2022-rgtqw | Distributed Desalination using Solar Energy: A Techno-economic Framework to Decarbonize Nontraditional Water Treatment | Desalination of nontraditional waters (e.g., agricultural drainage, brackish groundwater, industrial discharges, etc.) using renewable energy sources offers a possible route to transform our incumbent linear consumption model (discharge after use) to a circular one (beneficial reuse). This transition will also shift desalination from large-scale centralized coastal facilities towards modular distributed treatment plants (~1000 m3/day) in inland locations. This new scale of desalination can be satisfied using solar energy to decarbonize water production, but additional considerations, such as storage to address intermittency and inland brine management to address high disposal costs, become important. In this work, we evaluate the levelized cost of water or LCOW for 16 solar desalination technologies (with different generation–storage-desalination–brine management subsystems) at 2 different salinities corresponding to nontraditional sources. For fossil fuel-driven desalination plants at the distributed scale, we find that zero liquid discharge is economically favorable to inland brine disposal. For renewable desalination, we discover that (i) solar-thermal energy is better suited to both membrane and thermal desalination plants compared to photovoltaics largely due to the low cost of thermal storage, and that (ii) energy storage, despite its higher cost, outperforms water storage on a levelized basis as the latter has a low utilization factor with intermittently operated desalination plants. The analysis also yields a promising
outlook for the LCOW of solar desalination by 2030 as the costs of solar generation and energy storage decrease to meet the U.S. Department of Energy targets. Finally, we highlight subsystem cost and performance targets for solar desalination to achieve cost parity with fossil fuel-driven
water treatment. | Akanksha Menon; Mingxin Jia; Sumanjeet Kaur; Chris Dames; Ravi Prasher | Energy; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Water Purification; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63081623eadd9a7fa381c0a2/original/distributed-desalination-using-solar-energy-a-techno-economic-framework-to-decarbonize-nontraditional-water-treatment.pdf |
6798982c81d2151a0243770f | 10.26434/chemrxiv-2025-vt7tq | The Chemistry and Biology of the Tetrodotoxin Natural Product Family | Tetrodotoxin is a neurotoxic marine alkaloid, first isolated in 1909 from pufferfish and named after the biological order tetraodontiformes. Since its structural elucidation in 1964, it has attracted the interest of synthetic organic chemists due to its exceptional polarity, complex architecture, and important biological activity. This review highlights the diversity of the tetrodotoxin natural product family and discusses the origins of derivatives, biosynthetic hypotheses, and biological activities. Furthermore, potential therapeutic applications and structure-activity relationship studies are covered, along with the total syntheses of the natural product and selected derivatives that were published to date. | Benedikt Nißl; Marcel Mülbaier; Francesca Grisoni; Dirk Trauner; Marcel Bermúdez; Clemens Dialer; David Konrad | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6798982c81d2151a0243770f/original/the-chemistry-and-biology-of-the-tetrodotoxin-natural-product-family.pdf |
67802a75fa469535b95e480d | 10.26434/chemrxiv-2024-gstxb-v3 | Mechanism of DNA Chemical Denaturation | We developed a method to evaluate the degree of influence of electrostatic repulsion and different attraction forces on DNA during its chemical denaturation. Our method can be suitable for selecting DNA (or other systems with controllable denaturation) targeted for specific applications and/or to optimize the denaturants for any given DNA. Our theory has been developed for DNA chemical denaturation for low and medium denaturation degrees, including but not limited to 50\% denaturation as a reversible first-order reaction. Specifically, we show the degrees of influence of hydrogen bonding, dispersion, polar forces, proton donor/acceptor ratio, dipole induction, orientation parameter, and electrostatic interaction on the denaturation process of DNA. The absolute enthalpy values for DNA chemical denaturation are significantly lower than those in the thermal denaturation process (positive). We show that the mechanism for reaching 50\% DNA denaturation differs thermally and chemically. The thermal denaturation process mainly involves breaking hydrogen bonds via heating DNA, while the chemical denaturation process involves replacing the hydrogen bonding of DNA with denaturants. We also show that hydrogen bonding is the most significant part of the enthalpy of chemical denaturation for the T4 bacteriophage DNA, and the proton-donor effect is the dominant mechanism in disrupting hydrogen bonds in DNA denaturation. The influence of this effect is two times greater than that of the proton-acceptor effect. We also show that another essential factor for DNA denaturation is the orientation component, which is part of the polar cohesion parameter. We show that the total cohesion parameter measured at 50\% of DNA chemical denaturation represents the electrostatic (repulsion) forces that maintain the DNA helix. The conclusions above were achieved using the cohesive energy density approach and corresponding equations based on the thermodynamics of the denaturation process. Independent experimental data, which we analyzed using our theory, supported these conclusions. | Daniel Ostrovsky; Mikhail Ostrovsky | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67802a75fa469535b95e480d/original/mechanism-of-dna-chemical-denaturation.pdf |
6666e43b409abc034512a6d6 | 10.26434/chemrxiv-2024-8kbh6 | Spectroscopic Characterization of the Complexes of 2-(2′-Pyridyl)-Benzimidazole and (H2O)1,2, (CH3OH)1,2, and (NH3)1,2 Isolated in the Gas Phase | The present article presents a comprehensive laser spectroscopic characterization of 2-(2′-Pyridyl)-Benzimidazole (PBI)-S1,2 complexes (S = H2O, CH3OH, and NH3) isolated in the gas phase. The study aimed to understand docking preference of small molecules on N-bearing bio-relavent multifunctional molecules. Based on the LIF and R2PI spectroscopy, we have identified two distinct isomers of 1:1 (PBI-H2O) and 1:2 (PBI-(H2O)2) complexes. In the cases of PBI-CH3OH and PBI-NH3 systems, a single 1:1 and 1:2 complex was identified in each case. Computational analyses predicted the most stable structure, labelled as PBI-S-a with NIH···S and SH···NP (NIH = imidazolyl NH and NP: Pyridyl-N) hydrogen bonds at site-a. The structures were associated with significantly higher stability of the S1 state (D0(S1)>D0(S0)) compared to that in the corresponding ground states. The structure of PBI-H2O-b isomer, with CPH···S and SH···NI hydrogen bonds, was characterized by a blue-shifted band origin transition, validating computational predictions. The PBI-(S)2-aa (S=H2O, CH3OH, and NH3) isomers exhibited large red-shifted S0→S1 band origins, as predicted computationally. A unique PBI-(H2O)2-ab isomer was detected with a significantly lowered redshifted band origin transition compared to the aa-isomer, in which a solvent molecule is bound to the sites a and b PBI molecule. Notably, PBI-H2O complexes exhibit solvent-to-chromophore proton transfer reactions, with varying energy barriers depending on the isomeric configuration. The energy barriers for proton transfer reactions in PBI-H2O-b isomers demonstrated significantly elevated barriers (> 800 cm-1). In PBI-(H2O)-aa, the energy barrier (>436 cm-1) is marginally elevated from 420±10 cm-1 in PBI-H2O-a isomer. This study enhances the understanding of complex molecular interactions and provides insights into the excited-state processes, laying the groundwork for further investigations. | Arkaprabha Sen; Saurabh Khodia; Ramesh Jarupula; Simran Baweja; Bhavika Kalal; Surajit Maity | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6666e43b409abc034512a6d6/original/spectroscopic-characterization-of-the-complexes-of-2-2-pyridyl-benzimidazole-and-h2o-1-2-ch3oh-1-2-and-nh3-1-2-isolated-in-the-gas-phase.pdf |
63e665f31d2d184063406919 | 10.26434/chemrxiv-2023-3ld59 | De novo design of lipopeptide-based fusion inhibitor as potential broad-spectrum antiviral agent | The recent surge in emerging viral infections warrants the need to design broad-spectrum antivirals. We aimed to develop a lead molecule that targets the membrane to block fusion, an obligate step of enveloped virus infection. The approach is based on the Coronin-1 protein of Mycobacterium, which presumably inhibits the phagosome-lysosome fusion, and a unique Trp-Asp (WD) sequence is placed at the distorted -meander motif. We have designed a WD-based branched lipopeptide that supports C=OHN hydrogen-bonding, the tryptophan-tryptophan - stacking, and the intermolecular H-bonding between COO and CO2H groups. These cooperative interactions are expected to create a -sheet-like supramolecular assembly at the membrane surface, which increases the interfacial order, and decreases the water penetration. Myr-D(WD)2 was shown to block artificial membrane fusion completely. We demonstrated that the Myr-D(WD)2 supramolecular organization can restrict the infection from H1N1, H9N2, murine coronavirus, and human coronavirus (HCoV-OC43). Together, the present study provided an evidence-based broad-spectrum antiviral potential of a designed small lipopeptide. | Pradip Kumar Tarafdar; Avijit Sardar; Sucharita Bhowmick; Mithila Kamble; Bibhas Hazra; Nikesh Dewangan; Amirul Islam Mallick | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e665f31d2d184063406919/original/de-novo-design-of-lipopeptide-based-fusion-inhibitor-as-potential-broad-spectrum-antiviral-agent.pdf |
621f9416c6bb5580d079effd | 10.26434/chemrxiv-2022-7g2qs | The Influence of molecular design on structure-property relationships of a supramolecular polymer prodrug | Supramolecular self-assemblies of hydrophilic macromolecules functionalized with hydrophobic, structure-directing components have long been used for drug delivery. In these systems, loading of poorly soluble compounds is typically achieved through physical encapsulation during or after formation of the supramolecular assembly, resulting in low encapsulation efficiencies and limited control over release kinetics that are predominately governed by diffusion and carrier degradation. To overcome these limitations, amphiphilic prodrugs that leverage a hydrophobic drug as both the therapeutic and structure-directing component can be used to create supramolecular materials with higher loading and controlled release kinetics when biodegradable or enzymatically cleavable linkers are used. Here, we report the design, synthesis, and characterization of a library of supramolecular polymer prodrugs based on poly(ethylene glycol) (PEG) and the pro-regenerative drug 1,4-dihydrophenonthrolin-4-one-3-carboxylic acid (DPCA). Structure-property relationships were elucidated through experimental characterization of prodrug behavior in both the wet- and dry-state, using scattering techniques and electron microscopy, and corroborated by coarse-grained modeling. Molecular architecture and hydrophobic-to-hydrophilic ratio of PEG-DPCA conjugates strongly influenced their physical state in water, ranging from fully soluble to supramolecular assemblies of micelles and nanofibers. Molecular design and supramolecular structure, in turn, were shown to dramatically alter hydrolytic and enzymatic release, bioactivity, and cellular transport of DPCA. In addition to potentially expanding therapeutic options for DPCA through control of supramolecular assemblies, the resulting design principles elaborated here may inform the development of other supramolecular prodrugs based on hydrophobic small molecule compounds. | Kelsey G. DeFrates; Joakim Engström; Nivedina A. Sarma; Athiyya Umar; Jisoo Shin; Jing Cheng; Ahmad K. Omar; Phillip Messersmith | Biological and Medicinal Chemistry; Polymer Science; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621f9416c6bb5580d079effd/original/the-influence-of-molecular-design-on-structure-property-relationships-of-a-supramolecular-polymer-prodrug.pdf |
60c74663469df42650f4363b | 10.26434/chemrxiv.11310293.v1 | Characterization of Glycosyl Dioxolenium Ions and Their Role in Glycosylation Reactions | Controlling the
chemical glycosylation reaction remains the major challenge in the synthesis of
oligosaccharides. Though 1,2-<i>trans</i> glycosidic linkages can be installed using
neighboring group participation, the construction of 1,2-<i>cis</i> linkages is
difficult and has no general solution. Long-range participation (LRP) by distal
acyl groups may steer the stereoselectivity, but contradictory results have
been reported on the role and strength of this stereoelectronic effect. It has
been exceedingly difficult to study the bridging dioxolenium
ion
intermediates because of their high reactivity and fleeting nature. Here we report
an integrated approach, using infrared ion spectroscopy, DFT calculations and a
systematic series of glycosylation reactions to probe these ions in detail. Our study reveals how distal acyl groups can
play a decisive role in shaping the stereochemical outcome of a glycosylation
reaction and opens new avenues to exploit these species in
the assembly of oligosaccharides and glycoconjugates to fuel biological
research | Thomas Hansen; Hidde Elferink; Jacob M.A. van Hengst; Kas Houthuijs; Wouter A. Remmerswaal; Alexandra Kromm; Giel Berden; Stefan van der
Vorm; Anouk Rijs; Herman S. Overkleeft; Dmitri Filippov; Floris P. J. T. Rutjes; Gijsbert van der Marel; Jonathan Martens; Jos Oomens; Jeroen D. C. Codée; Thomas Boltje | Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74663469df42650f4363b/original/characterization-of-glycosyl-dioxolenium-ions-and-their-role-in-glycosylation-reactions.pdf |
62b5227c1278ae145dedb964 | 10.26434/chemrxiv-2022-mxwc5-v2 | The Intermolecular Interactions of Pyrene and its Oxides in Toluene Solution |
In this work, the Conformer-Rotamer Ensemble Sampling Tool, (CREST) with the underlying semi-empirical GFN2-xtb method was used for automated geometry exploration of the homodimers of pyrene, pyrene-4,5-dione, and pyrene-4,5,9,10- tetraone, along with the heterodimer of pyrene and pyrene-4,5,9,10-tetraone. Geometries and energies of the dimers were further refined at the ωB97X-D4/def2-TZVP level of theory, both in gas phase, and in toluene solution. Computations in solu- tions were handled using the CPCM (Conductor-like Polarizible Continuum Model) and SMD (Solvation Model based on Density) models. Two previously unidentified pyrene-homodimer conformations are identified, and the effects of oxidation on the geometries and energies of dimerization are explored; in general, oxidation leads to stronger intermolecular interactions, and decreased solubility in toluene. For selected dimers, DLPNO-CCSD(T)/cc-pVTZ/SMD(Toluene) energies are determined at the DFT geometries, and illustrate the accuracy of the ωB97X-D4 approach, with an MAD of 1.47 kJ/mol. | Nathanael J. King; Alex Brown | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b5227c1278ae145dedb964/original/the-intermolecular-interactions-of-pyrene-and-its-oxides-in-toluene-solution.pdf |
628cf7c7809e32d2db9b222a | 10.26434/chemrxiv-2021-ppdtb-v3 | Cyclometalated Iridium-Coumarin Ratiometric Oxygen Sensors: Improved Signal Resolution and Tunable Dynamic Ranges | In this work we introduce a new series of ratiometric oxygen sensors for hypoxic environments based on phosphorescent cyclometalated iridium centers partnered with organic coumarin fluorophores. Three different cyclometalating ligands and two different pyridyl-containing coumarin types were used to prepare six target complexes with tunable excited-state energies. Three of the complexes display dual emission, with fluorescence arising from the coumarin ligand, and phosphorescence from either the cyclometalated iridium center or the coumarin. These dual-emitting complexes function as ratiometric oxygen sensors, with the phosphorescence is quenched under O₂ while fluorescence is unaffected. The use of blue-fluorescent coumarins results in good signal resolution between fluorescence and phosphorescenc. Moreover, the sensitivity and dynamic range, measured with Stern-Volmer analysis, can be tuned two orders of magnitude by virtue of our ability to synthetically control the triplet excited-state ordering. The complex with cyclometalated irdium 3MLCT phosphorescence operates under hyperoxic conditions, whereas the two complexes with coumarin-centered phosphorescence are sensitive to very low levels of O¬2 and function as hypoxic sensors. | Yanyu Wu; Gregory D. Sutton; Michael D. S. Halamicek; Xinxin Xing; Jiming Bao; Thomas S. Teets | Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Spectroscopy (Inorg.); Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628cf7c7809e32d2db9b222a/original/cyclometalated-iridium-coumarin-ratiometric-oxygen-sensors-improved-signal-resolution-and-tunable-dynamic-ranges.pdf |
664f2d4a91aefa6ce1cb7bc9 | 10.26434/chemrxiv-2024-0q4b8-v2 | Chemical Open-Loop Recycling of Polyethylene | The scientific challenge currently receiving much attention is the catalytic conversion of non-biodegradable polymers into versatile chemical platform molecules. As a model of a chemical upcycling process, we have developed a homogeneous catalytic system to break down persistent polyethylene waste into valuable chemical intermediates that could ultimately be used to produce important chemical products, including environmentally friendly, biodegradable plastics. In the first step, a smart pyrolysis of polyolefin waste yields oils, containing long-chain olefins as the major components. Then, for the next transformation step, tailored BICAAC-Ru olefin metathesis catalysts were used in combination with an alkene isomerization catalyst (RuHCl(CO)(PPh3)3) for the transformation of the pyrolysis oil to propylene via isomerization metathesis (ISOMET) reaction in ethylene atmosphere. Eventually, translation of the highly efficient single-metal catalyst system enabled ISOMET reaction to a 900 mL reactor setup and repetitive batch experiments could prove the long-term stability of the catalyst system and the highest turn over number (TON = 3800) reported so far for propylene using polyethylene municipal waste feedstock. Propylene content in the gas phase achieved the 20 vol%. Ultimately, these results pave the way for the large-scale applicability of this process as a relevant demonstration of the combined application of adapted catalyst design and chemical engineering optimization with the aim of establishing a multi-dimensional circular economy concept in the chemical industry. | Vajk Farkas; Pascal Albrecht; Ádám Erdélyi; Márton Nagyházi; Beatrix Csutorás; Gábor Turczel; Norbert Miskolczi; Janka Bobek-Nagy; Ole Osterthun; Jürgen Klankermayer; Róbert Tuba | Catalysis; Organometallic Chemistry; Chemical Engineering and Industrial Chemistry; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664f2d4a91aefa6ce1cb7bc9/original/chemical-open-loop-recycling-of-polyethylene.pdf |
63c7210323c13b56df130fe6 | 10.26434/chemrxiv-2022-qz1zl-v2 | Photochemical Upconversion in Solution: The Role of Oxygen and Magnetic Field Response | Upconversion processes effectively convert two or more low energy photons into one higher energy photon, and have diverse applications in photovoltaics and biomedicine. Upconversion is generally spin-selective, and its magnetic field response can be used to examine the interplay between two different mechanisms for photochemical upconversion in solution: triplet-triplet annihilation, and singlet-oxygen mediated energy transfer. A kinetic model is developed and applied to explain the different photoluminescence profiles of oxygenated versus deoxygenated systems. From the magnetic field response, the triplet-triplet annihilation rate constant is estimated. The conditions required to maximize upconversion photoluminescence intensity in oxygenated solution are determined. | Roslyn Forecast; Francesco Campaioli; Timothy W. Schmidt; Jared H. Cole | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Chemical Kinetics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c7210323c13b56df130fe6/original/photochemical-upconversion-in-solution-the-role-of-oxygen-and-magnetic-field-response.pdf |
6568d40c5bc9fcb5c9c05388 | 10.26434/chemrxiv-2023-d2wdr | Synthesis and properties of allylic, benzylic, propargylic and allenylic oxonium ions | Despite numerous studies of trialkyloxonium ions in the literature, investigations into the chemistry of allylic, benzylic, propargylic and allenylic oxonium ions are rare. Existing reports on well characterized allylic and benzylic oxonium ions invariably construct these species based on constrained tricyclic oxatriquinane/oxatriquinacene scaffolds, and only one example of an unconstrained but thermally highly unstable benzylic oxonium ion has been reported in the literature without detailed characterization. Herein we report an investigation on a collection of allylic, benzylic and hitherto unknown propargylic and allenylic oxonium ions prepared on unconstrained scaffolds by a general, modular and unified strategy. Permutation of the substitution pattern of these oxonium ions allowed the extension of the strategy for the syntheses of various doubly-substituted oxonium ions. Most of these oxonium ions could be characterized at room temperature by NMR, and a series of unexpected reactions and chemical behavior pertinent to these species are briefly described. | Hau Sun Sam Chan; Yingzi Li; Jack L. Sutro; Daniel S. Brown; Robert S. Paton; Jonathan W. Burton | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6568d40c5bc9fcb5c9c05388/original/synthesis-and-properties-of-allylic-benzylic-propargylic-and-allenylic-oxonium-ions.pdf |
60fac8718804431689e3155b | 10.26434/chemrxiv-2021-dpbdx | Exploration of the chemical space of DNA-encoded libraries | DNA-Encoded Library (DEL) technology has emerged as an alternative method for bioactive molecule discovery in medicinal chemistry. It enables simple synthesis and screening of compound libraries of enormous size. Even though it gains more and more popularity each day, there are almost no reports of chemoinformatics analysis of DEL chemical space. Therefore, in this project we aimed to generate and analyze theultra-large chemical space of DEL. Around 2500 DELs were designed using commercially available BBs resulting in 2,5B DEL compounds that were compared to biologically relevant compounds from ChEMBL using Generative Topographic Mapping. This allowed to choose several optimal DELs covering the chemical space of ChEMBL to the highest extent and thus containing the maximum possible percentage of biologically relevant chemotypes. Different combinations of DELs were also analyzed to identify a set of mutually complementary libraries allowing to attain even higher coverage of ChEMBL than it is possible with one single DEL. | Yuliana Zabolotna; Regina Pikalyova; Dmitriy Volochnyuk; Dragos Horvath; Gilles Marcou; Alexandre Varnek | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fac8718804431689e3155b/original/exploration-of-the-chemical-space-of-dna-encoded-libraries.pdf |
644fc2fc6ee8e6b5ed680740 | 10.26434/chemrxiv-2023-hht0b | Assembly of six types of heteroleptic Pd2L4 cages under kinetic control | Difficulty in multi-component self-assembly under thermodynamic control arises from increasing the number of possible isomers with similar thermodynamic stabilities. Past efforts on multi-component self-assembly of metal-organic cages have mainly focused on finding a suitable combination of building blocks to lead to a single multi-component self-assembly as the thermodynamically most stable product. Here, we present another approach to selectively produce multi-component Pd(II)-based self-assemblies under kinetic control based on the selective ligand exchanges of weak Pd–L coordination bonds retaining the original orientation of the metal centers in a kinetically stabilized cyclic structure and on local reversibility given in a certain area of the energy landscape in the presence of the assist molecule that facilitates error correction of coordination bonds. The kinetic approach enabled us to build all six types of Pd2L4 cages and heteroleptic tetranuclear cages composed of three kinds of ditopic ligands. Though the cage complexes thus obtained are metastable, they are stable for 1 month or more at room temperature. | Tsukasa Abe; Naoki Sanada; Keisuke Takeuchi; Atsushi Okazawa; Shuichi Hiraoka | Inorganic Chemistry; Supramolecular Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2023-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644fc2fc6ee8e6b5ed680740/original/assembly-of-six-types-of-heteroleptic-pd2l4-cages-under-kinetic-control.pdf |
635acc361db0bd43c33c4980 | 10.26434/chemrxiv-2022-lxgvr-v2 | Bio-weathering Using Shewanella oneidensis MR-1 Enhances Selective Recovery of Rare Earth Elements from Alaskan Coal Mines | Coal mines in Alaska with high rare earth elements (REEs) levels (286-524 mg/kg) serve as an alternative domestic source for REEs. Existing leaching/separation technologies fail to selectively recover REEs from the feedstock and require downstream multiple purification stages that increase the overall operational cost. This study aims at bio-weathering coal from two Alaskan coal mines (Wishbone Hill and Healy) at three density fractions (1.3 float, and 1.3 and 1.5 sink) using Shewanella oneidensis MR-1 for achieving higher selective REEs recovery in one-step process. Optimizing the bio-weathering process by varying solids percentages (5.7 to14.3% w/v), particle size (-14 to -200 M), incubation temperatures (30 to 34 °C), and inoculum dosing (0.2 to 1% v/v) resulted in highest recovery of Neodymium (75.3%) and total REEs (98.4%) from 1.3 float Wishbone Hill and 1.3 sink Healy coal, respectively. When compared to the chemical leaching process, bio-weathering enhanced selective recovery of REEs including Scandium, Yttrium, Ytterbium, Terbium, Erbium, and Lutetium from Healy coal at low density, and Yttrium from Wishbone Hill coal at high density. The results indicate the future scope for developing cost-effective selective REEs recovery processes that may address the global critical minerals supply chain risk. | Ankur Sachan; Subhabrata Dev; Brandon R Briggs; Tathagata Ghosh; Srijan Aggarwal; Fahimeh Dehghani | Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Lanthanides and Actinides; Minerals; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635acc361db0bd43c33c4980/original/bio-weathering-using-shewanella-oneidensis-mr-1-enhances-selective-recovery-of-rare-earth-elements-from-alaskan-coal-mines.pdf |
60c749d3bdbb89d858a3926c | 10.26434/chemrxiv.12114642.v1 | Atomic-Scale Variations of Interfacial Water Structure Driven by Site-Specific Chemistry | <p>Although
interfacial solution structure impacts environmental, biological and
technological phenomena, including colloidal stability, protein assembly,
heterogeneous nucleation, and water desalination, its molecular details remain
poorly understood. Here, we visualize the three-dimensional (3D) hydration
structure at the boehmite(010)-water interface using fast force mapping (FFM). Using
a self-consistent scheme to decouple long-range tip-sample interactions from
short-range solvation forces, we obtain the solution structure with lattice
resolution. The results are benchmarked against molecular dynamics simulations
that explicitly include the effects of the tip with different levels of approximation
and systematically account for tip size, chemistry, and confinement effects. We
find four laterally structured water layers within one nanometer of the surface,
with the highest water densities at sites adjacent to hydroxyl groups. The
findings reveal a complex relationship between site-specific chemistry, water
density, and long-range particle interactions; and represent a major step
forward towards quantitative data interpretation and widespread implementation
of 3D FFM.</p> | Elias Nakouzi; Andrew G Stack; S.N. Kerisit; Benjamin A Legg; Christopher J. Mundy; Gregory K. Schenter; Jaehun Chun; James De Yoreo | Interfaces; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d3bdbb89d858a3926c/original/atomic-scale-variations-of-interfacial-water-structure-driven-by-site-specific-chemistry.pdf |
62b1f03ce84dd13a0dfd1eba | 10.26434/chemrxiv-2022-lj2k0 | Virtual Research Group Modules: Scalable Simulations of STEM Research | Laboratory research experiences can be an important part of the training process for STEM professionals, but barriers exist that can prevent broad access to these opportunities. Virtual Research Group (VRG) modules, which use data curated from the scientific literature to simulate aspects of the research process, provide a scalable alternative to traditional in-lab research experiences. Here we describe the general concept of VRG modules and the implementation of a VRG module focused on block copolymers in both a high school outreach program and an undergraduate materials science course. Through qualitative and quantitative data analysis of student post-survey responses, we demonstrate that VRG modules effectively simulate many of the attributes of traditional research experiences. We also compare student experiences when VRG modules are offered in three different formats: (i) competitive in-person, (ii) competitive virtual, and (iii) collaborative virtual. Finally, we demonstrate that VRGs can be applied to topics other than block copolymers through implementation of a VRG module on bulk metallic glass. | Marissa Tousley; Ariana Dyer; Michael Grzenda; Dylan Kovacevich; Jonathan Singer | Materials Science; Chemical Education; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b1f03ce84dd13a0dfd1eba/original/virtual-research-group-modules-scalable-simulations-of-stem-research.pdf |
623b29bfa4ed9572d92a8b92 | 10.26434/chemrxiv-2022-wmn75 | The missing intermediate in the catalytic cycle of [FeFe]-hydrogenases: Diiron site reduced state featuring a bridging CO ligand observed at room temperature | The metalloenzymes hydrogenases are natures redox catalyst for molecular hydrogen (H2) uptake and production. In [FeFe]-hydrogenases catalysis is facilitated at a unique diiron site. The two iron ions are connected by an azadithiolate bridging ligand (−SCH2NHCH2S−, ADT) and coordinated by a CO and CN− ligand each. Upon reduction of this diiron site the ligand arrangement of a third CO ligand is heavily debated. Two main geometries that differ by the origin of a bridging ligand in between the iron ions and the occupation of a free binding site are discussed. In a first scenario a hydride is bound in the bridging position and the third CO ligand occupies the open coordination site resulting in a geometry not favourable for catalysis. Experimental data indicative of the latter case has been collected at room temperature. In a second scenario the third CO ligand occupies a position in between the two iron ions resulting in a free coordination site favoured for H2 catalysis. Here up to date, experimental data indicative of this geometry, in particular the infrared band of the bridging CO (µCO) ligand, has only been observed at cryogenic temperatures questioning its catalytic relevance. In this study, we characterise the diiron site reduced intermediate that features the µCO geometry and preserves the open coordination site via FTIR spectroscopy at room temperature. The observation of this proposed diiron site reduced reaction intermediate with µCO geometry at room temperature makes its involvement in H2 catalysis more likely. | Moritz Senger; Holly Redman; Marco Lorenzi; Gustav Berggren | Physical Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Biocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623b29bfa4ed9572d92a8b92/original/the-missing-intermediate-in-the-catalytic-cycle-of-fe-fe-hydrogenases-diiron-site-reduced-state-featuring-a-bridging-co-ligand-observed-at-room-temperature.pdf |
60c75103337d6c18bde28463 | 10.26434/chemrxiv.13072397.v2 | Reduced Fouling Ultrafiltration Membranes via In-Situ Polymerisation Using Polydopamine Functionalised Titanium Oxide | The trade-off phenomenon between selectivity and permeation flux is a major challenge
in pressure-driven membranes, and specifically for ultrafiltration membranes. Currently, many
research studies have been performed to try to increase permeability while maintaining the
rejection at a high level. However, in most of these studies, the improvement of permeability
was accompanied by a decrease in rejection or vice versa. To tackle this problem, TiO2
nanoparticles were attached on the surface of PES membranes using polydopamine as adhesive
agent. In general, it is quite challenging to attach/bind TiO2 on the surface of membranes due
to agglomeration of nanoparticles. Therefore, we developed a practical, simple and a scalable
method to attach TiO2 nanoparticles (NPs) on the top surface of membrane using one-step dip
coating. Experimental results revealed that the modified layer enhanced the hydrophilicity of
the PES UF membranes as confirmed by the decrease of contact angle from. As a result, the
modified membranes exhibited a significant improvement in anti-fouling properties, with 12
times higher water permeation flux (962 LMH for pDA-f-TiO2-PES30) as compared to the
pristine PES membranes (79.9 LMH). The static adsorption of BSA on the surface of
membranes was reduced from (60 µg/cm2 for pristine PES to 21 µg/cm2 for pDA-f-TiO2-
PES120).
Furthermore, the modified PES membranes displayed a higher flux recovery ratio (97%) and
fouling reversibility (98.62%) than pristine PES membrane (37.63%). Also, the coated PES
membranes bestowed a good antibacterial property relative to the pristine one. Besides, the
membranes showed better physical and chemical stability as compared with unmodified PES
membranes. Thus, this study provided a facile approach for enhancing the anti-fouling
performance of PES ultrafiltration membranes. | Muayad al-Shaeli; Hanaa M. Hegab; Xiya Fang; Lizhong He; Chang Liu; Huanting Wang; Kaisong Zhang; Bradley P. Ladewig | Composites; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75103337d6c18bde28463/original/reduced-fouling-ultrafiltration-membranes-via-in-situ-polymerisation-using-polydopamine-functionalised-titanium-oxide.pdf |
628143a6809e32f74a90df38 | 10.26434/chemrxiv-2022-65l6j | Finite Element Modelling of the Combined Faradaic and Electrostatic Contributions to the Voltammetric Response of Monolayer Redox Films | The voltammetric response of electrodes coated with a redox-active monolayer is computed by finite element simulations based on a generalized model that couples the Butler-Volmer, Nernst-Planck and Poisson equations. The model yields a full description of the electric potential and charge distributions across the monolayer and into the bulk solution, including the potential distribution associated with ohmic resistance in the bulk solution. In this way, it is possible to properly account for electrostatic effects at the molecular film/electrolyte interface, which are present due to the changing charge states of the redox head groups as they undergo electron transfer, under both equilibrium and non-equilibrium conditions. Our numerical simulations also significantly extend previous theoretical predictions by simultaneously including both the effects of finite electron-transfer rates and electrolyte conductivity. Distortion of the voltammetric wave due to ohmic potential drop in the solution is shown to be a function of the supporting electrolyte concentration and scan rate, in agreement with experimental observations. The electric potential and charge distributions across an electrochemically inactive monolayer and into the solution are also simulated as a function of applied potential and are found to agree with the Gouy-Chapman-Stern theory, allowing numerical predictions of the capacitive background currents in voltammetric experiments. | Katherine Levey; Martin Edwards; Henry White; Julie Macpherson | Physical Chemistry; Analytical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Processes; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628143a6809e32f74a90df38/original/finite-element-modelling-of-the-combined-faradaic-and-electrostatic-contributions-to-the-voltammetric-response-of-monolayer-redox-films.pdf |
61ff6515a6fb4dc0384c687c | 10.26434/chemrxiv-2022-qx28k | Nonequilibrium Regulation of Interfacial Chemistry for Dissipative Supramolecular Assembly of Macroscopic Hydrogels | The nonequilibrium assembly in nature exists at the microscopic and macroscopic scales, and represents the most common way to regulate object motions by consuming chemical fuels. In artificial nonequilibrium systems, most of the work has focused on the microscopic dissipative assembly, whereas the investigation on nonequilibrium assembly of macroscopic building blocks is rarely reported. Here, we present an efficient strategy to dynamically mediate the interfacial chemistry of pH-responsive polyelectrolyte hydrogels, thereby regulating their macroscopic nonequilibrium assembly. The driving force for the assembly is the transient electrostatic attraction, which is regulated by the biocatalytic feedback-driven temporal programming of the pH of the system. The dissipative assembly process can be controlled by adjusting the hydrogel parameters and fuel composition and it can be repeated by refueling the system. Most importantly, the ordered sewing of complementary hydrogels promotes the precise nonequilibrium supramolecular assembly to yield transient macroscopic supramolecular devices potentially useful for timed release. | Ting Zhao; Yuyu E; Jiwei Cui; Jingcheng Hao; Xu Wang | Materials Science; Polymer Science; Aggregates and Assemblies; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ff6515a6fb4dc0384c687c/original/nonequilibrium-regulation-of-interfacial-chemistry-for-dissipative-supramolecular-assembly-of-macroscopic-hydrogels.pdf |
610aa85c30231a7ef90382c7 | 10.26434/chemrxiv-2021-74mkk | Binary-QSAR guided virtual screening of FDA approved drugs and compounds in clinical investigation against SARS-CoV-2 main protease | With the emergence of the new SARS-CoV-2 virus, drug repurposing studies have gained substantial importance. Combined with the efficacy of recent improvements in ligand- and target-based virtual screening approaches, virtual screening has become faster and more productive than ever. In the current study, an FDA library of approved drugs and compounds under clinical investigation were screened for their antiviral activity using the MetaCoreTM/MetaDrugTM (https://portal.genego.com) platform's antiviral therapeutic activity binary QSAR model. In the 6733-compound collection, we found 370 compounds with a normalized therapeutic activity value greater than a cutoff of 0.75. Only these selected compounds were used for molecular docking studies against the SARS-CoV-2 Main Protease (Mpro). After initial short (10 ns) molecular dynamics (MD) simulations with the top-50 docked compounds and following Molecular Mechanics Generalized Born Surface Area (MM/GBSA) calculations, top-10 compounds were subjected to longer (100 ns) MD simulations and end-point MM/GBSA estimations. Our virtual screening protocol yielded Cefuroxime pivotexil, an ester prodrug of second-generation cephalosporin antibiotic Cefuroxime, as being a considerable molecule for drug repurposing against the SARS-CoV-2 Mpro. | Serdar Durdagi; Lalehan Oktay; Ece Erdemoglu; Ilayda Tolu; Yesim Yumak; Aysenur Ozcan; Elif Acar; Sehriban Buyukkilic; Alpsu Olkan | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610aa85c30231a7ef90382c7/original/binary-qsar-guided-virtual-screening-of-fda-approved-drugs-and-compounds-in-clinical-investigation-against-sars-co-v-2-main-protease.pdf |
60c755c4bdbb893105a3a8cb | 10.26434/chemrxiv.12275603.v10 | Changes in criteria air pollution levels in the US before, during, and after Covid-19 stay-at-home orders: evidence from regulatory monitors | <p>The widespread and rapid social and economic changes from Covid-19 response might be expected to dramatically improve air quality. However, national monitoring data from the US Environmental Protection Agency for criteria pollutants (PM2.5, ozone, NO2, CO, PM10) provide inconsistent support for that expectation. Specifically, during stay-at-home orders, average PM2.5 levels were slightly higher (~10% of its multi-year interquartile range [IQR]) than expected; average ozone, NO2, CO, and PM10 levels were slightly lower (~30%, ~20%, ~27%, and ~1% of their IQR, respectively) than expected. The timing of peak anomaly, relative to the stay-at-home orders, varied by pollutant (ozone: 2 weeks before; NO2, CO: 3 weeks after; PM10: 2 weeks after); but, by 5-6 weeks after stay-at-home orders, the concentration anomalies appear to have ended. For PM2.5, ozone, CO, and PM10, no US state had lower-than-expected pollution levels for all weeks during stay-at-home-orders; for NO2, only Arizona had lower-than-expected levels for all weeks during stay-at-home orders. Our findings show that the enormous changes from the Covid response have not lowered PM2.5 levels across the US beyond their normal range of variability; for ozone, NO2, CO, and PM10 concentrations were lowered but the reduction was modest and transient. <br /></p> | Bujin Bekbulat; Joshua S. Apte; Dylan B Millet; Allen Robinson; Kelley C. Wells; Julian D. Marshall; Albert Presto | Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755c4bdbb893105a3a8cb/original/changes-in-criteria-air-pollution-levels-in-the-us-before-during-and-after-covid-19-stay-at-home-orders-evidence-from-regulatory-monitors.pdf |
60c747a74c89198238ad2d85 | 10.26434/chemrxiv.11760519.v1 | Cobalt/Lewis Acid Catalysis for Hydrocarbofunctionalization of Alkynes via Cooperative C–H Activation | A catalytic system comprised of a cobalt-diphosphine complex and a Lewis acid (LA) such as AlMe3 has been found to promote hydrocarbofunctionalization reactions of alkynes with Lewis basic and electron-deficient substrates such as formamides, pyridones, pyridines, and azole derivatives through site-selective C-H activation. Compared with known Ni/LA catalytic system for analogous transformations, the present catalytic system not only feature convenient set up using inexpensive and bench-stable precatalyst and ligand such as Co(acac)3 and 1,3-bis(diphenylphosphino)propane (dppp), but also display distinct site-selectivity toward C-H activation of pyridone and pyridine derivatives. In particular, a completely C4-selective alkenylation of pyridine has been achieved for the first time. Mechanistic stidies including DFT calculations on the Co/Al-catalyzed addition of formamide to alkyne have suggested that the reaction involves cleavage of the carbamoyl C-H bond as the rate-limiting step, which proceeds through a ligand-to-ligand hydrogen transfer (LLHT) mechanism leading to an alkyl(carbamoyl)cobalt intermediate. | Chang-Sheng Wang; Sabrina Monaco; Anh Ngoc Thai; Md. Shafiqur Rahman; Chen Wang; Naohiko Yoshikai | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747a74c89198238ad2d85/original/cobalt-lewis-acid-catalysis-for-hydrocarbofunctionalization-of-alkynes-via-cooperative-c-h-activation.pdf |
60c75415bb8c1a059c3dc18d | 10.26434/chemrxiv.13606700.v1 | Aerobically Stable and Substitutionally Labile α-Diimine Rhenium Dicarbonyl Complexes | New
synthetic routes to aerobically stable and substitutionally labile a-diimine rhenium(I) dicarbonyl complexes are
described. The molecules are prepared in high yield from the <i>cis-cis-trans-</i>[Re(CO)<sub>2</sub>(<i><sup>t</sup></i>Bu<sub>2</sub>bpy)Br<sub>2</sub>]<sup>-</sup>
anion (<b>2</b>, where<b> </b><i><sup>t</sup></i>Bu<sub>2</sub>bpy
is 4,4'-di-<i>tert</i>-butyl-2,2'-bipyridine),
which can be isolated from the one electron reduction of the corresponding
17-electron complex (<b>1</b>). Compound <b>2 </b>is stable in the solid state, but in
solution it is oxidized by molecular oxygen back to <b>1</b>. Replacement of a single bromide of <b>2</b> by s-donor monodentate ligands (Ls) yields stable
neutral 18-electron <i>cis-cis-trans-</i>[Re(CO)<sub>2</sub>(<i><sup>t</sup></i>Bu<sub>2</sub>bpy)Br(L)]
species. In coordinating solvents like methanol the halide is replaced giving
the corresponding solvated cations. [Re(CO)<sub>2</sub>(<i><sup>t</sup></i>Bu<sub>2</sub>bpy)Br(L)] species can be further
reacted with Ls to prepare stable <i>cis-cis-trans-</i>[Re(CO)<sub>2</sub>(<i><sup>t</sup></i>Bu<sub>2</sub>bpy)(L)<sub>2</sub>]<sup>+</sup>
complexes in good yield. Ligand substitution of Re(I) complexes proceeds via pentacoordinate intermediates
capable of Berry pseudorotation. In addition to the <i>cis-cis-trans-</i>complexes, <i>cis-cis-cis-</i>
(all cis) enantiomers are also
formed. In particular, <i>cis-cis-trans-</i>[Re(CO)<sub>2</sub>(<i><sup>t</sup></i>Bu<sub>2</sub>bpy)(L)<sub>2</sub>]<sup>+</sup>
complexes establish an equilibrium with all cis enantiomers in solution. The
solid state crystal structure of nearly all molecules presented could be
elucidated. The molecules adopt a slightly distorted octahedral geometry. In
comparison to similar <i>fac</i>-[Re(CO)<sub>3</sub>]<sup>+</sup>complexes,
Re(I) diacarbonyl species are characterized by a bend (ca. 7°) of the axial ligands towards the a-diimine unit. [Re(CO)<sub>2</sub>(<i><sup>t</sup></i>Bu<sub>2</sub>bpy)Br<sub>2</sub>]<sup>-</sup> and [Re(CO)<sub>2</sub>(<i><sup>t</sup></i>Bu<sub>2</sub>bpy)Br(L)] complexes may be considered
as synthons for the preparation of a variety of new stable
diamagnetic dicarbonyl rhenium <i>cis-</i>[Re(CO)<sub>2</sub>]<sup>+</sup> complexes,
offering a convenient entry in the chemistry of the core. | Kevin Schindler; Aurélien Crochet; Fabio Zobi | Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75415bb8c1a059c3dc18d/original/aerobically-stable-and-substitutionally-labile-diimine-rhenium-dicarbonyl-complexes.pdf |
62bdaeb7f51939440379b1d3 | 10.26434/chemrxiv-2022-kzrzz | Chiral and Achiral Pendant-Bound Poly(biphenylylacetylene)s Bearing Amide and/or Carbamate Groups: One-Handed Helix Formations and Chiral Recognition Abilities | A series of cis-poly(biphenylylacetylene) (PBPA) derivatives bearing chiral and achiral pendant groups at the 4’-position of the biphenyl units through an amide (–NHCO–) or carbamate (–NHCOO–) linker were synthesized by polymerization of the corresponding biphenylylacetylene (BPA) monomers that can be readily prepared in one step from a novel amino-functionalized BPA. An excess one-handed helix induction in the PBPAs through covalent and noncovalent chiral interactions and their chiral recognition abilities when used as chiral stationary phases (CSPs) for high-performance liquid chromatography (HPLC) were investigated. PBPAs bearing optically-pure L-amino acid residues showed unique two-state helical conformational changes between the extended and contracted helices regulated by the solvent-mediated on/off switching of the intramolecular hydrogen-bonding formations between the pendants or at each pendant. The chiral recognition abilities of the helical PBPAs were significantly influenced by the kinds of the pendant L-amino acid residues. The preferred-handed contracted helical PBPA carrying an L-leucine derived pendant showed an excellent chiral resolving power toward various racemic compounds including axially and point chiral compounds and chiral metal complexes. The elution orders of some racemates were completely reversed when its helical conformation was changed to the extended helix. On the other hand, the trans-enriched nonhelical L-leucine-bound PBPA derived from its preferred-handed cis-helical PBPA and achiral pendant-bound cis-helical PBPAs induced by noncovalent chiral interactions and subsequent static memory of the helicity showed a poor and no chiral recognition, respectively. | Tomoyuki Ikai; Shogo Okuda; Motoki Aizawa; Eiji Yashima | Polymer Science; Conducting polymers; Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bdaeb7f51939440379b1d3/original/chiral-and-achiral-pendant-bound-poly-biphenylylacetylene-s-bearing-amide-and-or-carbamate-groups-one-handed-helix-formations-and-chiral-recognition-abilities.pdf |
6659be8e91aefa6ce174aa2b | 10.26434/chemrxiv-2024-bqd8c | Navigating a 1E+60 Chemical Space | Herein we report a virtual library of 1E+60 members, a common estimate for the total size of the drug-like chemical space. The library is obtained from 100 commercially available peptide and peptoid building blocks assembled into linear or cyclic oligomers of up to 30 units, forming molecules within the size range of peptide drugs and accessible by solid-phase synthesis. We demonstrate ligand-based virtual screening (LBVS) using the peptide design genetic algorithm (PDGA), which evolves a population of 50 members to resemble a given target molecule using molecular fingerprint similarity as fitness function. Target molecules are reached in less than 10,000 generations. Like in many journeys, the value of the chemical space journey using PDGA lies not in reaching the target but in the journey itself, here by encountering molecules otherwise difficult to design. We also show that PDGA can be used to generate median molecules and analogs of non-peptide target molecules. | Markus Orsi; Jean-Louis Reymond | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6659be8e91aefa6ce174aa2b/original/navigating-a-1e-60-chemical-space.pdf |
6787437981d2151a0231c5f7 | 10.26434/chemrxiv-2025-5kgvt | GC-MS-based metabolomics – Part 1
Gas chromatography-mass spectrometry (GC-MS) and its place in the plant metabolomics toolbox | Metabolomics, which is typically referred to as the post-genomic methodology addressing low molecular weight metabolites, became a powerful tool in post-genomic research over the last two decades. Indeed, the state of the art metabolomics relies on several well-established complemen-tary platforms – nuclear magnetic resonance (NMR) spectroscopy, liquid and gas chromatog-raphy coupled on-line to mass spectrometry (LC- and GC-MS, respectively), capillary electropho-resis-mass spectrometry (CE-MS). Among them, GC-MS represents one of the oldest and most well-established techniques currently employed in metabolomics of volatile compounds and non-volatiles – polar low-molecular weight metabolites, which can be efficiently converted in volatile form by comprehensive derivatization of polar functional groups. Currently, GC-MS is recog-nized as the core analytical technique in characterization of plant primary metabolome, although the other methods contribute to the whole metabolite profile essentially. Therefore, here we ad-dress the role of GC-MS in plant metabolomics and its potential for profiling of low molecular weight metabolites. Further, we comprehensively review the methods of sample preparation with a special emphasis on the extraction and derivatization approaches, which are currently employed to improve the method performance and its metabolome coverage. | Nadezhda Frolova; Anastasia Orlova; Veronika Popova; Tatiana Bilova; Andrej Frolov | Biological and Medicinal Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6787437981d2151a0231c5f7/original/gc-ms-based-metabolomics-part-1-gas-chromatography-mass-spectrometry-gc-ms-and-its-place-in-the-plant-metabolomics-toolbox.pdf |
678a8de5fa469535b96b9c82 | 10.26434/chemrxiv-2025-c4515 | Comparative analysis of Im7 dynamics with polarizable and non-polarizable CHARMM family of force fields | Electrostatic interactions are fundamental to biomolecular structure, stability, and function. While these interactions are traditionally modeled using fixed-charge force fields, such approaches are not transferable among different molecular environments. Polarizable force fields, such as DRUDE, address this limitation by explicitly incorporating polarization effect. However, their performance does not uniformly surpass that of nonpolarizable force fields, since multiple factors such as bonded terms, dihedral correction maps, and solvent screening also modulate biomolecular dynamics. In this work, we study the Im7 protein to evaluate the structural and dynamic behaviors of non-polarizable (CHARMM36m) and polarizable (DRUDE2019) force fields relative to NMR experiments. Our simulations show that DRUDE better stabilizes α-helices than CHARMM36m, including shorter ones that contain helix-breaking residues. However, both force fields underestimate loop dynamics, particularly in the loop I region, due mainly to restricted dihedral angle sampling. Moreover, salt bridge population and dynamics reveal that DRUDE and CHARMM36m preferentially stabilize different salt-bridges. This variability arises from the interplay of ionic interactions, charge screening by the environment, and the flexibility of neighboring residues. Additionally, the latest DRUDE2019 variant, featuring updated NBFIX and NBTHOLE parameters for ion-protein interactions, demonstrated improved accuracy in modeling Na+-protein interactions. These findings highlight the need to balance bonded and non-bonded interactions along with dihedral correction maps while incorporating polarization effects to improve the accuracy of force fields to model protein structure and dynamics. | Sangram Prusty; Rafael Bruschweiler; Qiang Cui | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a8de5fa469535b96b9c82/original/comparative-analysis-of-im7-dynamics-with-polarizable-and-non-polarizable-charmm-family-of-force-fields.pdf |
67766107fa469535b98877da | 10.26434/chemrxiv-2024-1r9tb-v2 | (Semi-) Automatic Review Process for Common Compound Characterization Data in Organic Synthesis | A method for data review in chemical sciences with a focus on data for the characterization of synthetic molecules is described. As current procedures for data curation in chemistry rely almost exclusively on manual checking or peer reviewing, a (semi-)automatic procedure for the evaluation of data assigned to molecular structures is proposed and demonstrated. The information usually required for the identification of isolated compounds is used to clarify whether the data is complete with respect to the available data types and metadata, if it is consistent with the proposed structure and if it is plausible in comparison to simulated data. Spectra prediction and automatic signal comparison are applied to NMR evaluation, mass spectrometry data are evaluated by signal extraction, and machine learning is used for IR analysis. The proposed protocol shows how an integration of different tools for data analysis can help to overcome the challenges of the currently purely manual review and curation efforts for analytical data in synthetic chemistry. | Yu-Chieh Huang; Pierre Tremouilhac; Stefan Kuhn; Pei-Chi Huang; Chia-Lin Lin; Nils Schlörer; Oskar Taubert; Markus Götz; Nicole Jung; Stefan Bräse | Organic Chemistry; Analytical Chemistry; Chemical Education; Organic Synthesis and Reactions; Analytical Chemistry - General; Chemoinformatics | CC BY 4.0 | CHEMRXIV | 2025-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67766107fa469535b98877da/original/semi-automatic-review-process-for-common-compound-characterization-data-in-organic-synthesis.pdf |
6222939897f2103d33fd8368 | 10.26434/chemrxiv-2021-00kkd-v2 | Understanding MOF nucleation from solution with Evolving Graphs | Metal-Organic Frameworks (MOFs) exhibit attractive characteristics for separations such as remarkable surface area and diverse porosities. However, a mechanistic understanding of their synthesis and scale-up remains underexplored due to the complicated nature of building block interactions. In this work, we investigate the collective assembly of building units that have been experimentally observed to initiate MOF nucleation, using MIL-101(Cr) as a prototypical example. We use large-scale molecular dynamics simulations under a variety of synthesis conditions and mixture compositions. We observe that the choice of solvent (water or DMF), introduction of ions (Na+, F-) and the relative population of MIL-101(Cr) half-secondary building unit (half-SBU) isomers has a strong influence on the cluster formation process. In more detail, the shape, size, nucleation and growth rates, crystallinity and short and long-range order largely vary depending on the synthesis conditions. We evaluate these properties as they naturally emerge when interpreting self-assembly of MOF nuclei as the time-evolution of an undirected graph. Solution-induced con-formational complexity and ionic concentration have a dramatic effect on the morphology of clusters emerging during assembly, such diversity is captured by key features of the graph representation. More precisely, pure solvent leads to rapid formation of a small number of large clusters, while ions result in slower nucleation through smaller clusters in water. Finally, we use Principal Component Analysis (PCA) on graph properties to successfully deconvolute MOF self-assembly into a small number of molecular descriptors, such as the average coordination number between half-SBUs and fractal dimension, which can be followed by time-resolved spectroscopy. We conclude that graph theory can be used to understand complex processes such as MOF nucleation through providing molecular descriptors accessible by both simulation and experiment. | Loukas Kollias; Roger Rousseau; Vassiliki-Alexandra Glezakou; Matteo Salvalaglio | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Processes; Self-Assembly; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6222939897f2103d33fd8368/original/understanding-mof-nucleation-from-solution-with-evolving-graphs.pdf |
6634e7f7418a5379b05a51ac | 10.26434/chemrxiv-2024-t2s9p | GRAM-SCALE ENZYMATIC SYNTHESIS OF 2'-DEOXYRIBONUCLEOSIDE ANALOGUES USING NUCLEOSIDE TRANSGLYCOSYLASE | Nucleosides are pervasive building blocks that are found throughout nature and used extensively in medicinal chemistry and biotechnology. However, the preparation of base-modified analogues using conventional synthetic methodology poses challenges in scale-up and purification. In this work, an integrated approach, involving structural analysis, screening and reaction optimisation, was established for the preparation of 2'-deoxyribonucleoside analogues catalyzed by the Type II nucleoside 2'-deoxyribosyltransferase from Lactobacillus leichmannii (LlNDT-2). Structural analysis, in combination with substrate profiling, identified the constraints on pyrimidine and purine acceptor bases by LlNDT2. A solvent screen identifies pure water as a suitable solvent for the preparation of high value purine and pyrimidine 2'-deoxyribonucleoside analogues on a gram scale under optimised reaction conditions. This approach provides the basis to establish a convergent, step-efficient chemoenzymatic platform for the preparation of high value 2'-deoxyribonucleosides. | Admir Salihovic; Alex Ascham; Andrea Taladriz-Sender; Samantha Bryson; Jamie Withers; Iain McKean; Paul Hoskisson; Gideon Grogan; Glenn Burley | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioorganic Chemistry; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6634e7f7418a5379b05a51ac/original/gram-scale-enzymatic-synthesis-of-2-deoxyribonucleoside-analogues-using-nucleoside-transglycosylase.pdf |
6442cec083fa35f8f6069726 | 10.26434/chemrxiv-2023-wzv3q | AL4GAP: Active Learning Workflow for generating DFT-SCAN Accurate Machine-Learning Potentials for Combinatorial Molten Salt Mixtures | Machine learning interatomic potentials have emerged as a powerful tool for bypassing the spatio-temporal limitations of ab initio simulations, but major challenges remain in their efficient parameterization. We present AL4GAP, an active learning software workflow for generating multi-composition Gaussian approximation potentials (GAP) for arbitrary molten salt mixtures. The workflow capabilities includes: (1) setting up user-defined combinatorial chemical spaces of charge neutral mixtures of arbitrary molten mixtures spanning 11 cations (Li, Na, K, Rb, Cs, Mg, Ca, Sr, Ba and two heavy species, Nd and Th) and 4 anions (F, Cl, Br and I), (2) configurational sampling using low-cost empirical parameterizations, (3) ensemble active learning for down-selecting configurational samples for single point density functional theory calculations at the level of strongly constrained and appropriately normed (SCAN) exchange-correlation functional, and (4) Bayesian optimization for hyperparameter tuning of two-body and many-body GAP models. We apply the workflow to showcase high throughput generation of five independent GAP models for multi-composition binary-mixture melts, each of increasing complexity with respect to charge valency and electronic structure, namely: LiCl-KCl, NaCl-CaCl2, KCl-NdCl3, CaCl2-NdCl3 and KCl-ThCl4. Our results indicate that GAP models, can accurately predict structure for diverse molten salt mixture with DFT-SCAN accuracy, capturing the intermediate range ordering characteristic of the multi-valent cationic melts. | Jicheng Guo; Vanessa Woo; David Andersson; Nathaniel Hoyt; Mark Williamson; Ian Foster; Chris Benmore; Nicholas Jackson; Ganesh Sivaraman | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Theory - Computational; Machine Learning; Energy Storage | CC BY 4.0 | CHEMRXIV | 2023-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6442cec083fa35f8f6069726/original/al4gap-active-learning-workflow-for-generating-dft-scan-accurate-machine-learning-potentials-for-combinatorial-molten-salt-mixtures.pdf |
62e0f291adb01e1810adf5ee | 10.26434/chemrxiv-2022-td42k | Orthogonally protected diaminocyclopentenones as versatile synthons: Total synthesis of (±)-Agelastatin A | Natural products containing amicyclopentanes are common secondary metabolites, often biologically active. This works aims at the preparation of a useful synthon containing orthogonally protected amines. To this end, furfural and two amines were employed to form mixed trans-4,5-diaminocyclopentenones promoted by Cu(OTf)2. The selected amines can be orthogonally deprotected, allowing selective modification of the amines on the cyclopentane core. Their utility was showcased for the total synthesis of highly complex (±)-Agelastatin A. | Rafael Gomes; Rafael Vale; Carlos Afonso | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e0f291adb01e1810adf5ee/original/orthogonally-protected-diaminocyclopentenones-as-versatile-synthons-total-synthesis-of-agelastatin-a.pdf |
6458f8df07c3f029376abd95 | 10.26434/chemrxiv-2023-szl7b | A Flexible Theory for Catalysis: Learning Alkaline Oxygen Reduction on Complex Solid Solutions within the Ag-Pd-Pt-Ru Composition Space | Compositionally complex materials such as high-entropy alloys and oxides have the potential to be efficient platforms for catalyst discovery because of the vast chemical space spanned by these novel materials. Identifying the composition of the most active catalyst materials, however, requires unraveling the descriptor-activity relationship, as experimental screening the multitude of possible element ratios quickly becomes a daunting task. In this work, we show that inferred adsorption energy distributions of *OH and *O on complex solid solution surfaces within the space spanned by the system Ag-Pd-Pt-Ru are coupled to the experimentally observed electrocatalytic performance for the oxygen reduction reaction. In total, the catalytic activity of 1582 alloy compositions is predicted with a cross-validated mean absolute error of 0.042 mA/cm2 by applying a theory-derived model with only two adjustable parameters. Trends in the discrepancies between predicted electrochemical performance values of the model and the measured values on thin film surfaces subsequently provide insight into the alloys’ surface compositions during reaction conditions. Bridging this gap between computationally modeled and experimentally observed catalytic activities, not only reveals insight into the underlying theory of catalysis but also takes a step closer to realizing exploration and exploitation of high-entropy materials. | Christian M. Clausen; Olga A. Krysiak; Lars Banko; Jack K. Pedersen; Wolfgang Schuhmann; Alfred Ludwig; Jan Rossmeisl | Theoretical and Computational Chemistry; Materials Science; Catalysis; Alloys; Theory - Computational; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6458f8df07c3f029376abd95/original/a-flexible-theory-for-catalysis-learning-alkaline-oxygen-reduction-on-complex-solid-solutions-within-the-ag-pd-pt-ru-composition-space.pdf |
63276d2b975e9440e67fb861 | 10.26434/chemrxiv-2022-8q749 | SIRT2i_Predictor: A machine learning-based tool to facilitate the discovery of novel SIRT2 inhibitors | Selective sirtuin 2 (SIRT2) inhibitors hold therapeutic promise for treatment of wide range of age-related diseases. Despite promising preclinical results, none of the SIRT2 inhibitors have reached clinical trials. In order to facilitate development of novel SIRT2 inhibitors, a machine learning based tool titled SIRT2i_Predictor was developed through this work. The main utility of SIRT2i_Predictor is to support virtual screening (VS) campaigns and facilitate the selection of candidates for in vitro and in vivo evaluation. Appealing web-based interface which allows visualization of structure-activity relationships makes SIRT2i_Predictor a valuable tool in the lead optimization projects as well. The tool was built on panel of high-quality machine learning regression-based and binary classification-based models for prediction of inhibitors potency, as well as multiclass classification-based models for predictions of inhibitors SIRT1-3 isoform selectivity. The regression and classification structure-activity relationship models were created for 1797 publicly available compounds by exploring combinations of 5 machine learning algorithms and 4 molecular representations. SIRT2i_Predictor was demonstrated to be able to screen around 200000 compounds in matters of minutes with comparable chemical space coverage to the structure-based VS. The tool was applied in screening of in-house database of compounds further corroborating the utility in prioritization of compounds for costly in vitro screening campaigns. The code of SIRT2i_Predictor is made available at https://github.com/echonemanja/SIRT2i_Predictor. | Nemanja Djokovic; Minna Rahnasto-Rilla; Nikolaos Lougiakis; Maija Lahtela-Kakkonen; Katarina Nikolic | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63276d2b975e9440e67fb861/original/sirt2i-predictor-a-machine-learning-based-tool-to-facilitate-the-discovery-of-novel-sirt2-inhibitors.pdf |
66d223bd20ac769e5f650d22 | 10.26434/chemrxiv-2023-5wbkr-v2 | The AABBA Graph Kernel: Atom–Atom, Bond–Bond, and Bond–Atom Autocorrelations for Machine Learning | Graphs are one of the most natural and powerful representations available for molecules; natural because they have an intuitive correspondence to skeletal formulas, the language used by chemists worldwide, and powerful, because they are highly expressive both globally (molecular topology) and locally (atom and bond properties). Graph kernels are used to transform molecular graphs into fixed-length vectors, which, based on their capacity of measuring similarity, can be used as fingerprints for machine learning (ML). To date, graph kernels have mostly focused on the atomic nodes of the graph. In this work, we developed a graph kernel based on atom–atom, bond–bond, and bond–atom (AABBA) autocorrelations. The resulting vector representations were tested on regression ML tasks on a dataset of transition metal complexes; a benchmark motivated by the higher complexity of these compounds relative to organic molecules. In particular, we tested different flavors of the AABBA kernel in the prediction of the energy barriers and bond distances of the Vaska’s complex dataset (Friederich et al., Chem. Sci., 2020, 11, 4584). For a variety of ML models, including neural net- works, gradient boosting machines, and Gaussian processes, we showed that AABBA outperforms the baseline including only atom–atom autocorrelations. Dimensionality reduction studies also showed that the bond–bond and bond–atom autocorrelations yield many of the most relevant features. We believe that the AABBA graph kernel can accelerate the exploration of large chemical spaces and inspire novel molecular representations in which both atomic and bond properties play an important role. | Lucía Morán-González; Jørn Eirik Betten; Hannes Kneiding; David Balcells | Theoretical and Computational Chemistry; Materials Science; Organometallic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d223bd20ac769e5f650d22/original/the-aabba-graph-kernel-atom-atom-bond-bond-and-bond-atom-autocorrelations-for-machine-learning.pdf |
60c749169abda25addf8cb64 | 10.26434/chemrxiv.12024402.v1 | Direct Imaging of Correlated Defect Nanodomains in a Metal-Organic Framework | <p>Defect engineering
can enhance key properties of metal-organic frameworks (MOFs). Tailoring the
distribution of defects, for example in correlated nanodomains, requires characterization
across length scales. However, a critical nanoscale characterization gap has
emerged between the bulk diffraction techniques used to detect defect
nanodomains and the sub-nanometre imaging used to observe individual defects. Here,
we demonstrate that the emerging technique of scanning electron diffraction
(SED) can bridge this gap. We directly image defect nanodomains in the MOF
UiO-66(Hf) over an area of ca. 1 000 nm and with a spatial resolution ca. 5 nm to
reveal domain morphology and distribution. Based on these observations, we suggest
possible crystal growth processes underpinning synthetic control of defect
nanodomains. We also identify likely dislocations and small angle grain
boundaries, illustrating that SED could be a key technique in developing the
potential for engineering the distribution of defects, or “microstructure”, in
functional MOF design.</p> | Duncan Johnstone; Francesca Firth; Clare P. Grey; Paul A. Midgley; Matthew Cliffe; Sean M. Collins | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749169abda25addf8cb64/original/direct-imaging-of-correlated-defect-nanodomains-in-a-metal-organic-framework.pdf |
60c756b1702a9bbb0c18c95f | 10.26434/chemrxiv.14307368.v1 | Multi and Single-Reference Methods for the Analysis of Multi-State Peroxidation of Enolates | In spite of being spin-forbidden, some enzymes are capable of catalyzing the incorporation of O<sub>2</sub> (<sup>3</sup>Σ<sup>−</sup><sub>g</sub>) to<br />organic substrates without needing any cofactor. It has been established that the process followed by these<br />enzymes starts with the deprotonation of the substrate forming an enolate. In a second stage, the peroxidation<br />of the enolate formation occurs, a process in which the system changes its spin multiplicity from a triplet state<br />to a singlet state. In this article, we study the addition of O<sub>2</sub> to enolates using state-of-the-art multi-reference<br />and single-reference methods. Our results confirm that intersystem crossing is promoted by stabilization of<br />the singlet state along the reaction path. When multi-reference methods are used, large active spaces are<br />required, and in this situation, Semistochastic Heat-Bath Configuration Interaction (SHCI) emerges as a<br />powerful method to study these multi-configurational systems and is in good agreement with LCCSD(T)<br />when the system is well-represented by a single-configuration.<br /><br /> | Pablo Ortega; Sara Gil-Guerrero; Anzhela Veselinova; Alexandre Zanchet; Lola González-Sánchez; Pablo G. Jambrina; Cristina Sanz-Sanz | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756b1702a9bbb0c18c95f/original/multi-and-single-reference-methods-for-the-analysis-of-multi-state-peroxidation-of-enolates.pdf |
67c8002a6dde43c90890613c | 10.26434/chemrxiv-2025-csjff | Identifying Potential Missteps of Machine Learning in Molecular Chemistry | Machine learning-based methods are widely used today in chemical tasks, particularly in drug design. Graph Convolutional Neural Networks (GCNNs) compete with one another in predicting chemical properties, achieving errors comparable with those of experimental measurements. However, the increasing complexity of data entry structures and the trend toward utilizing three-dimensional molecular geometries are rarely grounded in a thorough search for accurate conformations for input. In this study, we examined the stability of the state-of-the-art GCNN architecture for drug discovery and identified vulnerabilities related to the structural features of the compounds. We found that molecular weight significantly influenced the discrepancy between predicted and calculated HOMO-LUMO gap values. We demonstrated that high similarity between new molecules and the training dataset, as measured by Tanimoto indices, did not lead to a qualitative prediction of the model. In contrast, more dissimilar structures require adding less information to the training set for a successful active learning procedure. | Anastasiia Smirnova; Artem Mitrofanov | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c8002a6dde43c90890613c/original/identifying-potential-missteps-of-machine-learning-in-molecular-chemistry.pdf |
60c742634c891991c3ad2441 | 10.26434/chemrxiv.8258900.v1 | Outer Sphere Urea Hydrolysis by Bis-Nickel Complexes: Questioning the Urea Activation by the Urease Enzyme | Urease enzyme has a dinuclear nickel active centre that hydrolyze urea into carbon dioxide and ammonia. In this work, two bis-nickel urease models were synthesized, [Ni<sub>2</sub>L(OAc)] and [Ni<sub>2</sub>L(Cl)(Et<sub>3</sub>N)<sub>2</sub>], based on the Trost bis-Pro0Phenol ligand (L). Interestingly, both complexes produced ammonia from urea, in which the [Ni<sub>2</sub>L(OAc)] complex was ten times slower than urease, whereas the more labile complex [Ni<sub>2</sub>L(Cl)(Et<sub>3</sub>N)<sub>2</sub>],was only four times slower. The intermediates were evaluated both experimentally and theoretically, indicating that the [Ni<sub>2</sub>L(H<sub>2</sub>O)<sub>2</sub>]<sup>+</sup> intermediate is the most important to activate urea via an outersphere mechanism. Isocyanate was produced in a self-elimination mechanism. The reaction performed with different substrates indicated that the biomimetic complexes were able to hydrolyze isocyanate. The outersphere activation of urea by these complexes reals an alternative activation mechanism to be considered for the urease enzyme, not yet reported in the literature. . <br /> | Caterina Gruenwaldt Cunha Marques Netto; Christian O. Martins; Letícia K. Sebastiany; Alejandro López-Castillo; Rafael S. Freitas; LEANDRO H. ANDRADE; Henrique E. Toma | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Kinetics and Mechanism - Inorganic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742634c891991c3ad2441/original/outer-sphere-urea-hydrolysis-by-bis-nickel-complexes-questioning-the-urea-activation-by-the-urease-enzyme.pdf |
64b7feb7ae3d1a7b0dfeba80 | 10.26434/chemrxiv-2023-hrgfw | Completing and balancing database excerpted chemical reactions with a hybrid mechanistic - machine learning approach | Computer Aided Synthesis Planning (CASP) development of reaction routes requires understanding of complete reaction structures. However, most reactions in the current databases are missing reaction co-participants. Although reaction prediction and atom mapping tools can predict major reaction participants and trace atom rearrangements in reactions, they fail to identify the missing molecules to complete reactions. This is because these approaches are data-driven models trained on the current reaction databases which comprise of incomplete reactions. In this work, a workflow was developed to tackle the reaction completion challenge. This includes a heuristic-based method to identify the balanced reactions from reaction databases and complete some imbalanced reactions by adding candidate molecules. A machine learning masked language model (MLM) was trained to learn from reaction SMILES sentences of these completed reactions. The model predicted missing molecules for the incomplete reactions; a workflow analogous to predicting missing words in sentences. The model is promising for prediction of small and middle size missing molecules in incomplete reaction records. The workflow combining both the heuristic and the machine learning methods completed more than half of the entire reaction space. | Chonghuan Zhang; Adarsh Arun; Alexei Lapkin | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b7feb7ae3d1a7b0dfeba80/original/completing-and-balancing-database-excerpted-chemical-reactions-with-a-hybrid-mechanistic-machine-learning-approach.pdf |
652ed4d8bda59ceb9ac9161f | 10.26434/chemrxiv-2023-96xng | Evaluating the Economic and Environmental Benefits of Deploying a National-Scale, Thermo-Chemical Plastic Waste Upcycling Infrastructure in the United States | Existing plastic recycling infrastructure largely relies on mechanical recycling technologies, which are capable of processing only a small subset of waste plastics. Emerging chemical technologies can “upcycle” plastic waste by producing high-value products (e.g., olefins that can be used to produce virgin-grade polymers) and are more scalable, as they can process a broader range of waste plastics (e.g., complex mixtures obtained from post-consumer and post-industrial waste). In this work, we study the economic and environmental benefits of deploying an upcycling infrastructure in the continental United States for producing low-density polyethylene (LDPE) and polypropylene (PP) from post-consumer plastic waste. Our analysis aims to determine the market (economy) size that the infrastructure can create, the degree of circularity that it can achieve, prices for waste and derived products, and environmental benefits of diverting plastic waste from landfill and incineration facilities. The analysis is based on a computational framework that integrates techno-economic analysis, lifecycle assessment, and value chain (supply chain) optimization. Our results demonstrate that the infrastructure generates a market (economy) of nearly 20 billion USD; moreover, we show high market values of upcycled products propagate through the value chain to create positive prices for plastic waste (generating significant incentives for residents to provide their waste). In other words, upcycling technologies open opportunities for residents to receive compensation for providing their plastic waste (waste is a valuable commodity in the infrastructure). Our analysis also indicates that the infrastructure can achieve a degree of circularity of 34% (relative to the total rates of residential plastic waste produced) and leads to significant environmental benefits over alternative waste disposal methods (decreases greenhouse gas emissions of incineration by 69-75\% and avoids the deployment of 86 new landfills over the next 50 years). Uncertainty analysis also reveals that the economy generated by the infrastructure is robust (remains viable) under various externalities (e.g., technology efficiencies, capital investment budgets, and polymer market values). | Evan Erickson; Jiaze Ma; Philip Tominac; Horacio Aguirre-Villegas; Victor Zavala | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Petrochemicals; Reaction Engineering | CC BY 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652ed4d8bda59ceb9ac9161f/original/evaluating-the-economic-and-environmental-benefits-of-deploying-a-national-scale-thermo-chemical-plastic-waste-upcycling-infrastructure-in-the-united-states.pdf |
6567efa229a13c4d474dfba4 | 10.26434/chemrxiv-2023-577n9 | Janus SEGPHOS: Integrating Persistent Photogenic Radicaloids with Multiple Circularly Polarized Doublet Radiance and Long-persistent Triplet Phosphorescence | Organic phosphors integrating circularly polarized persistent luminescence (CPPL) across the visible range are prevalent for applications in optical information encryption, bioimaging, and 3D display, but the pursuit of color-tunable CPPL in a single-component organics remains a formidable task. Herein, via in-suit photo-implanting radical ion-pairs into axial chiral crystals, we present and elucidate an unprecedented double-module decay strategy to achieve a colorful CPPL through a combination of stable triplet emission from neutral diphosphine and doublet radiance from photogenic radicals in an exclusive crystalline framework. Owing to the photoactivation-dependent doublet radiance component and an inherent triplet phosphorescence in the asymmetric environment, the CPL vision can be regulated by altering the photoactivation and observation time window, allowing colorful glow tuning from blue and orange to delayed green emission. Mechanism studies reveal that this asymmetric electron migration environment and hybrid n-π*, π-π* instincts serve an afterglow and radical radiance at ambient conditions. Moreover, we demonstrate the applications of colorful CPPL for displays and encryptions via manipulation of both excitation and observation time. | Bo Yang; Suqiong Yan; Shirong Ban; Yuan Zhang; Hui Ma; Fanda Feng; Wei Huang | Physical Chemistry; Materials Science; Aggregates and Assemblies; Optical Materials; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6567efa229a13c4d474dfba4/original/janus-segphos-integrating-persistent-photogenic-radicaloids-with-multiple-circularly-polarized-doublet-radiance-and-long-persistent-triplet-phosphorescence.pdf |
667047e45101a2ffa8c799fc | 10.26434/chemrxiv-2024-x1rr1 | Single-Molecule Mechanoresistivity by Intermetallic Bonding | The metal-electrode interface is key to unlocking emergent behaviour in all organic electrified systems,
from battery technology to molecular electronics. In the latter, interfacial engineering has enabled
efficient transport, higher device stability, and novel functionality. Mechanoresistivity – the change in
electrical behaviour in response to a mechanical stimulus and a pathway to extremely sensitive force
sensors – is amongst the most studied phenomena in molecular electronics, and the molecule-electrode
interface plays a pivotal role in its emergence, reproducibility, and magnitude. In this contribution, we
show that organometallic molecular wires incorporating a Pt(II) cation show mechanoresistive
behaviour of exceptional magnitude, with conductance modulations of more than three orders of
magnitude upon compression by as little as 1 nm. We synthesised series of cyclometalated Pt(II)
molecular wires, and used scanning tunnelling microscopy – break junction techniques to characterise
their electromechanical behaviour. Mechanoresistivity arises from an interaction between the Pt(II)
cation and the Au electrode triggered by mechanical compression of the single-molecule device, and
theoretical modelling confirms this hypothesis. Our study provides a new tool for the design of functional
molecular wires by exploiting previously unreported ion-metal interactions in single-molecule devices,
and develops a new framework for the development of mechanoresistive molecular junctions. | Amit Sil; Chiara Spano; Yahia Chelli; Simon Higgins; Sara Sangtarash; Gianluca Piccinini; Mariagrazia Graziano; Richard Nichols; Hatef Sadeghi; Andrea Vezzoli | Physical Chemistry; Organometallic Chemistry; Nanoscience; Nanodevices; Interfaces; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667047e45101a2ffa8c799fc/original/single-molecule-mechanoresistivity-by-intermetallic-bonding.pdf |
642aef9cdb1a20696e758152 | 10.26434/chemrxiv-2023-s5dhp | Using Science as a Tool to Shape Political Opinion | This article critically reviews and contextualises a publication by Wagner et al. in Nature Food 3, 921-32 (2022), titled "Transfer of cannabinoids into the milk of dairy cows fed with industrial hemp could lead to Δ9-THC exposure that exceeds acute reference dose" | James C Callaway; Bernhard Richard Beitzke | Agriculture and Food Chemistry; Feed; Food | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642aef9cdb1a20696e758152/original/using-science-as-a-tool-to-shape-political-opinion.pdf |
67c4a5196dde43c9082c040d | 10.26434/chemrxiv-2025-65v0m | Modulation of Aβ1-40 and Aβ4-40 co-assembly by Zinc: getting closer to the biological reality | Alzheimer’s disease (AD), one of the most common neurodegenerative diseases worldwide, is characterised by the self-assembly of amyloid-β peptides (Aβ) in senile plaques, which are also rich in metal ions such as Cu and Zn. Here, we investigated the influence of Zn(II) ions on the self- and co-assembly of Aβ1-40 and the N-terminally truncated Aβ4-40 peptides, the two most prevalent Aβ peptides in the brain. The Zn(II) coordination site in the soluble model peptide Aβ4-16 was investigated for the first time through pH-dependent X-ray absorption spectroscopy and nuclear magnetic resonance measurements, suggesting the formation of two species around neutral pH, depending on the (de)protonation of the N-terminal amine. The Zn(II) affinity was assessed via robust competition experiments, showing that Aβ4-16 has a four-fold lower affinity than Aβ1-16. The self-assembly of Aβ1-40 and Aβ4 40, and their co-assembly were monitored in presence of various Zn(II) levels, which reveals an important concentration-dependent modulatory effect of Zn(II) ions. In particular, the interplay between Zn(II), Aβ1-40 and Aβ4-40, compared to either binary Zn-Aβx-40 systems, promotes the formation of ill-defined assemblies regarded as more toxic than fibrils. This study provides new more-biologically relevant insights on the complex interaction between Zn(II) ions and the two major forms of Aβ peptides detected in the senile plaques, underscoring their significance in the pathophysiology of AD. | Lucie de Cremoux; Enrico Falcone; David Schmitt; Ewelina Stefaniak; Marta D. Wiśniewska; Nicolas Vitale; Wojciech Bal; Christelle Hureau | Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c4a5196dde43c9082c040d/original/modulation-of-a-1-40-and-a-4-40-co-assembly-by-zinc-getting-closer-to-the-biological-reality.pdf |
62474b473b5f99325acbc269 | 10.26434/chemrxiv-2022-hvqnz-v2 | Hot-casting assisted liquid additive engineering for efficient and stable perovskite solar cells | High-performance inorganic-organic lead halide perovskite solar cells (PSCs) are often fabricated with a liquid additive such as dimethyl sulfoxide (DMSO) which retards crystallization and reduces roughness and pinholes in the perovskite layers. However, DMSO can be trapped during perovskite film formation and induce voids and undesired reaction byproducts upon later processing steps. Here, we show that we can reduce the amount of residual DMSO in as-spin-coated films significantly - by 30 times - through use of pre-heated substrates, or a so-called hot-casting method. Hot-casting increases the perovskite film thickness which allows us to reduce the perovskite solution concentration. By reducing the amount of DMSO in proportion to the concentration of perovskite precursors and using hot-casting, we are able to fabricate perovskite layers with improved perovskite-substrate buried interfaces by suppressing the formation of byproducts which increase trap density and accelerate degradation of the perovskite layers. The best-performing PSCs exhibit power conversion efficiency (PCE) of 23.4% (23.0% stabilized efficiency) under simulated solar illumination. Furthermore, encapsulated devices showed considerably reduced post-burn-in decay of -0.84% of initial efficiency per 100 h, retaining more than 80% and 93% of their initial and post-burn-in efficiencies after 800 h of operation with maximum power point tracking (MPPT) under high-power of ultraviolet-(UV-)containing continuous light exposure (overall power density of 1.1 sun with 2.6 times higher UV-region power density than AM 1.5G). | Hanul Min; Junnan Hu; Zhaojian Xu; Tianran Liu; Saeed-Uz-Zaman Khan; Kwangdong Roh; Yueh-Lin Loo; Barry Rand | Energy; Photovoltaics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62474b473b5f99325acbc269/original/hot-casting-assisted-liquid-additive-engineering-for-efficient-and-stable-perovskite-solar-cells.pdf |
662773d8418a5379b075dabf | 10.26434/chemrxiv-2024-w3kwn | Harnessing Liquid Crystal Attributes of Near-Unit Photoluminescent Benzothioxanthene Photosensitizers: Photophysical Profiling in Solution, Solid State, and Polymer Matrix Embedding | Liquid crystals (LCs) have garnered significant attention for their unique optical and electrical properties, making them promising candidates in various technological applications such as smart displays, sensors, telecommunications, biomedicals or wearable electronics. In this study, we explore the potential of several highly emissive benzothioxanthene imide (BTI) derivatives as LC materials with a focus on their robustness and temperature-stable emission behavior. By tailoring the molecular structure of BTIs, we have accomplished exceptional emissive properties while maintaining the inherent advantages of LCs, such as their self-organizing ability and responsive nature. We describe the formation of enantiotropic liquid crystals whose mesomorphic properties dependent on the nature, length, and position of the side chain. Moreover, we have investigated the thermal stability of their emission spectra over a wide range of temperature, highlighting their potential use in demanding conditions where precise optical performances are critical. Our findings underscore the importance of molecular design in achieving highly emissive LC materials with enhanced robustness and temperature stability, opening new avenues for the use of BTI derivatives. | Frederico Duarte; Korentin Morice; Tatiana Ghanem; Dario Puchan Sánchez; Philippe Blanchard; Clara S.B. Gomes; Santiago Herrero; Clement Cabanetos; Cristian Cuerva; José Luis Capelo-Martínez; Carlos Lodeiro | Organic Chemistry; Materials Science; Physical Organic Chemistry; Dyes and Chromophores; Liquid Crystals | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662773d8418a5379b075dabf/original/harnessing-liquid-crystal-attributes-of-near-unit-photoluminescent-benzothioxanthene-photosensitizers-photophysical-profiling-in-solution-solid-state-and-polymer-matrix-embedding.pdf |
67c1af7c81d2151a0270d169 | 10.26434/chemrxiv-2025-z4m8x | Tribenzoylarsine – a Benign Arsenic Precursor for InAs Nanocrystals | III-V semiconductor nanocrystals (NCs) have emerged as a viable, more benign alternative to state-of-the-art II-VI and IV-VI NCs, which are increasingly restricted due to the toxicity of the comprising elements. While great progress has been achieved for InP, covering the visible range, the development of infrared-emitting InAs NCs has been relatively low-paced. This is due to the synthetic challenges arising from the highly covalent bonding in InAs and the small choice of available arsenic sources, which are essentially limited to tris(trimethylsilyl)arsine and tris(dimethylamino)arsine. Most importantly, wider adoption of these syntheses is hampered by their reliance on hazardous pyrophoric and costly reagents. In this work, we report for the first time the multigram synthesis of tribenzoylarsine, which can be used as a novel nonvolatile, nonpyrophoric, and hence safer, precursor for metal arsenide nanoparticles. We demonstrate that tribenzoylarsine reacts with indium oleate without additional reducing agents yielding small (~2 nm) InAs NCs. By tuning synthesis parameters (in particular, the addi-tion of zinc oleate or using continuous injection) it is possible to cover the photoluminescence range of 630–780 nm with full width at half maximum as low as 170–210 meV, which is a very competitive value to the existing synthetic approaches. Along with the significantly safer nature of tribenzoylarsine and the great potential for synthesis optimization, this makes it a very promising alternative to the currently used arsenic precursors. | Artsiom Antanovich; Volodymyr Shamraienko; Jannika Lauth; Vladimir Lesnyak | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1af7c81d2151a0270d169/original/tribenzoylarsine-a-benign-arsenic-precursor-for-in-as-nanocrystals.pdf |
673fafbf7be152b1d03fc318 | 10.26434/chemrxiv-2024-qdd0n | Deaminative ring contraction for the modular synthesis of pyrido[n]helicenes | A modular strategy involving the use of tertiary amines as templates to build multiple carbon–carbon bonds via reductive cyclization and deaminative contraction steps enables the scalable synthesis of (di)aza[5]helicenes and (di)aza[6]helicenes. The methods permit the rapid and gram-scale assembly of pyridyl-containing biaryl-linked dihydro-azepines as key intermediates that are advanced using a developed deaminative contraction reaction to access N-atom positional isomers of pyrido[5] and [6]helicenes. A telescoped synthesis that foregoes the purification of biaryl-linked dihydroazepines intermediates demonstrates expedited access to (±)-1-aza[6]helicene, a resolvable helicene valued for its circularly polarized luminescence properties. | Zachary Schwartz; Chelsea Valiton; Myles Lovasz; Farah Sadat; Michelle Phan; Ryan VanderLinden; Thomas Richmond; Andrew Roberts | Organic Chemistry; Materials Science; Organometallic Chemistry; Organic Synthesis and Reactions; Optical Materials; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673fafbf7be152b1d03fc318/original/deaminative-ring-contraction-for-the-modular-synthesis-of-pyrido-n-helicenes.pdf |
6527cfb4bda59ceb9a6a88bb | 10.26434/chemrxiv-2023-s7fbl | A High Efficiency Gas Phase Photoreactor for
Eradication of Methane from Low-Concentration
Sources | Despite the urgent need, very few methods are able to efficiently remove methane from waste air with low cost and energy per unit volume, especially at the low concentrations found in emissions from e.g. wastewater treatment, livestock production, biogas production and mine ventilation. We present the first results of a novel method based on using chlorine atoms in the gas phase, thereby
achieving high efficiency. A laboratory prototype of the Methane Eradication Photochemical System (MEPS) technology achieves 58% removal efficiency with a flow capacity of 30 L/min; a reactor volume of 90 L; UV power input at 368 nm of 110 W; chlorine concentration of 99 ppm; and a methane concentration of 55 ppm; under these conditions the apparent quantum yield (AQY) ranged from 0.48 to 0.56% and the volumetric energy consumption ranged from 36 to 244 kJ/m3. The maximum achieved AQY with this system was 0.83%. A series of steps that can
be taken to further improve performance are described. These metrics show that MEPS has the potential to be a viable method for eliminating low-concentration
methane from waste air. | Morten Krogsbøll; Hugo S. Russell; Matthew S. Johnson | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Agriculture and Food Chemistry; Atmospheric Chemistry; Environmental Science; Natural Resource Recovery | CC BY NC 4.0 | CHEMRXIV | 2023-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6527cfb4bda59ceb9a6a88bb/original/a-high-efficiency-gas-phase-photoreactor-for-eradication-of-methane-from-low-concentration-sources.pdf |
63494f0a86473a780212dd64 | 10.26434/chemrxiv-2022-7cztk | Cationic Tetrylene-Iron(0) Complexes: Access Points for Cooperative, Reversible Dihydrogen Activation and Open-Shell Iron(-I) Ferrato-Tetrylenes | The oxidative addition of catalytically relevant small molecules in molecular iron complexes poses a considerable challenge in achieving ‘precious metal catalysis’ utilizing this Earth abundant metal. Here, we show that non-innocent ligands based upon cationic heavier tetrylenes, EII (E = Ge, Sn), can work in synergy with a reactive iron center for the oxidative cleavage of inert bonds. Specifically, the open-shell cationic stannylene-iron(0) complex 4 (4 = [PhiPDippSn·Fe·IPr]+; PhiPDipp = {[Ph2PCH2Si(iPr)2](Dipp)N}; Dipp = 2,6-iPr2C6H3; IPr = [(Dipp)NC(H)]2C:) cleaves dihydrogen under very mild condi-tions (1.5 bar, 298K), in forming bridging hydrido-complex 6, which features a [Sn-(μ-H)2-Fe] core. This reaction is readily reversible, with hydrogen being entirely extruded after simple freeze-thaw degassing of reaction mixtures, regenerating 4. Computational investigation of the mechanism incites the ne-cessity of both the Fe0 and SnII centers in the key H-H bond scis-sion step. The related GeII system, 3, does not activate dihydro-gen. However, one-electron reduction of this species leads to clean oxidative addition of one C-P linkage of the PhiPDipp ligand in an intermediary Fe-I complex, leading to FeI phosphide species 7. In contrast, the same one-electron reduction reaction of 4 gives facile access to the iron(-I) ferrato-stannylene, 8. This presents strong evidence for the intermediacy of such a species in the reduction of 3, and represents an example of a covalently bound formal iron(-I) compound. EPR spectroscopy, SQUID magnetometry, and supporting computational analysis strongly indicate the high localization of electron spin density at Fe-I in this unique d9-iron complex. | Terrance Hadlington; Philip Keil; Ademola Soyemi; Kilian Weisser; Christian Limberg; Tibor Szilvasi | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Ligand Design; Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63494f0a86473a780212dd64/original/cationic-tetrylene-iron-0-complexes-access-points-for-cooperative-reversible-dihydrogen-activation-and-open-shell-iron-i-ferrato-tetrylenes.pdf |
650398fc99918fe537f6e6f3 | 10.26434/chemrxiv-2023-p9w5c | Gas-Phase and Solid-State Electronic Structure Analysis and DFT Benchmarking of HfCO | Ab initio multi-reference configuration interaction (MRCI) and coupled cluster singles doubles and perturbative triples [CCSD(T)] levels of theory were used to study ground and excited electronic states of HfCO. We report potential energy curves, dissociation energies (De), excitation energies, harmonic vibrational frequencies, and chemical bonding patterns of HfCO. The 3Ʃ– ground state of HfCO has an 1σ22σ21π2 electron configuration and a ~30 kcal/mol dissociation energy with respect to its lowest-energy fragments Hf(3F)+CO(X1Σ+). We further evaluated the De of its isovalent HfCX (X = S, Se, Te, Po) series and observed that they increase linearly from the lighter HfCO to the heavier HfCPo with the dipole moment of the CX ligand. The same linear relationship was observed for TiCX and ZrCX. We utilized the CCSD(T) benchmark values of De, excitation energy, and ionization energy (IE) values to evaluate density functional theory (DFT) errors with 23 exchange–correlation functionals spanning GGA, meta-GGA, global GGA hybrid, meta-GGA hybrid, range-separated hybrid, and double-hybrid functional families. The global GGA hybrid B3LYP and range-separated hybrid ωB97X performed well at representing the ground state properties of HfCO (De and IE). Finally, we extended our DFT analysis to the interaction of a CO molecule with a Hf surface and observed that the surface chemisorption energy and the gas-phase molecular dissociation energy are very similar for some DFAs but not others, suggesting moderate transferability of the benchmarks on these molecules to the solid-state. | Isuru Ariyarathna; Yeongsu Cho; Chenru Duan; Heather Kulik | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650398fc99918fe537f6e6f3/original/gas-phase-and-solid-state-electronic-structure-analysis-and-dft-benchmarking-of-hf-co.pdf |
60c75578469df4c3bdf45169 | 10.26434/chemrxiv.12923474.v2 | LigTMap: Ligand and Structure-Based Target Identification and Activity Prediction for Small Molecular Compounds | Motivation: Target prediction is a crucial step in modern drug discovery. However, existing
experimental approaches to target prediction are time-consuming and costly. <div>Results: The LigTMap server provides a fully automated workflow to identify targets from 17
target classes with >6000 proteins. It is a hybrid approach, combining ligand similarity search
with docking and binding similarity analysis, to predict putative targets. In the validation
experiment, LigTMap achieved a top-10 success rate of almost 70%, with an average precision
rate of 0.34. The class-specific prediction method improved the success rate further with enhanced
precision. In an independent benchmarking test, LigTMap showed good performance compared to
the currently best target prediction servers. LigTMap provides straightaway the PDB of a
predicted target and the optimal ligand binding mode, which could facilitate structure-based drug
design and the repurposing of existing drugs.
</div> | Faraz Shaikh; Hio Kuan Tai; Nirali Desai; Shirley Siu | Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75578469df4c3bdf45169/original/lig-t-map-ligand-and-structure-based-target-identification-and-activity-prediction-for-small-molecular-compounds.pdf |
64dce6764a3f7d0c0d4448eb | 10.26434/chemrxiv-2023-74vpv | Iodide Ozonolysis at the Surface of Aqueous Microdroplets | The ozonolysis of iodide occurs at the sea-surface and within sea-spray aerosol, influencing the overall ozone budget in the marine boundary layer and leading to the emission of reactive halogen gases. A detailed account of the surface mechanism has proven elusive, however, due to the difficulty in quantifying multiphase kinetics. To obtain a clearer understanding of this reaction mechanism at the air-water interface, we report pH-dependent ozonolysis kinetics of I- in single levitated microdroplets as a function of [O3] using a quadrupole electrodynamic trap and an open port sampling interface for mass spectrometry. A kinetic model, constrained by molecular simulations of O3 dynamics at the air-water interface, is used to understand the coupled diffusive, reactive, and evaporative pathways at the microdroplet surface, which exhibit a strong dependence on bulk solution pH. Under acidic conditions, the surface reaction is limited by O3 diffusion in the gas phase, whereas under basic conditions the reaction becomes rate limited on the surface. The pH dependence also suggests the existence of a reactive intermediate IOOO- as has previously been observed in the ozonolysis of Br-. Expressions for steady-state surface concentrations of reactants are derived and utilized to directly compute uptake coefficients for this system, allowing for an exploration of uptake dependence on reactant concentration. In the present experiments, reactive uptake coefficients of O3 scale weakly with bulk solution pH, increasing from 4×10-4 to 2×10-3 with decreasing solution pH from pH 13 to pH 3. | Alexander Prophet; Kritanjan Polley; Gary Van Berkel; David Limmer; Kevin Wilson | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Computational Chemistry and Modeling; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dce6764a3f7d0c0d4448eb/original/iodide-ozonolysis-at-the-surface-of-aqueous-microdroplets.pdf |
6323e2eeba8a6d53af50ef4b | 10.26434/chemrxiv-2022-1wscq-v2 | Single-molecule Magnetoluminescence from a Spatially Confined Persistent Diradical Emitter | Luminescent radicals are an emerging class of materials that exhibit unique photofunctions not found in closed-shell molecules due to their open-shell electronic structure. Particularly promising are photofunctions in which radical’s spin and luminescence are correlated; for example, when a magnetic field can affect luminescence (i.e., magnetoluminescence, ML). These photofunctions could be useful in the new science of spin photonics. However, previous observations of ML in radicals have been limited to systems in which radicals are randomly doped in host crystals or polymerized through metal complexation. This study shows that a covalently linked luminescent radical dimer (diradical) can exhibit the ML as a single-molecular property. This facilitates detailed elucidation of the requirements for and mechanisms of ML in radicals and can aid the rational design of ML-active radicals based on synthetic chemistry. | Ryota Matsuoka; Shojiro Kimura; Tomoaki Miura; Tadaaki Ikoma; Tetsuro Kusamoto | Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Optics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6323e2eeba8a6d53af50ef4b/original/single-molecule-magnetoluminescence-from-a-spatially-confined-persistent-diradical-emitter.pdf |
6647b37121291e5d1d8e8e2f | 10.26434/chemrxiv-2024-qp6qr | Free Energy Analysis of Peptide-Induced Pore Formation in Lipid Membranes by Bridging Atomistic and Coarse-Grained Simulations | Antimicrobial peptides (AMPs) are attractive materials for combating the antimicrobial resistance crisis because they can kill target microbes by directly disrupting cell membranes. Although thousands of AMPs have been discovered, their molecular mechanisms of action are still poorly understood. One broad mechanism for membrane disruption is the formation of membrane-spanning hydrophilic pores which can be stabilized by AMPs. In this study, we use molecular dynamics (MD) simulations to investigate the thermodynamics of pore formation in model single-component lipid membranes in the presence of one of three AMPs: aurein 1.2, melittin and magainin 2. To overcome the general challenge of modeling long timescale membrane-related behaviors, including AMP binding, clustering, and pore formation, we develop a generalizable methodology for sampling AMP-induced pore formation. This approach involves the long equilibration of peptides around a pore created with a nucleation collective variable by performing coarse-grained simulations, then backmapping equilibrated AMP-membrane configurations to all-atom resolution. We then perform all-atom simulations to resolve free energy profiles for pore formation while accurately modeling the interplay of lipid-peptide-solvent interactions that dictate pore formation free energies. Using this approach, we quantify free energy barriers for pore formation without direct biases on peptides or whole lipids, allowing us to investigate mechanisms of pore formation for these 3 AMPs that are a consequence of unbiased peptide diffusion and clustering. Further analysis of simulation trajectories then relates variations in pore lining by AMPs, AMP-induced lipid disruptions, and salt bridges between AMPs to the observed pore formation free energies and corresponding mechanisms. This methodology and mechanistic analysis have the potential to generalize beyond the AMPs in this study to improve our understanding of pore formation by AMPs and related antimicrobial materials. | Joshua Richardson; Reid Van Lehn | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Biophysics; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6647b37121291e5d1d8e8e2f/original/free-energy-analysis-of-peptide-induced-pore-formation-in-lipid-membranes-by-bridging-atomistic-and-coarse-grained-simulations.pdf |
60c753f1337d6c0909e28939 | 10.26434/chemrxiv.13109747.v2 | It's a Gas: Oxidative Dehydrogenation of Propane over Boron Nitride Catalysts | We investigate the role of gas-phase phenomena in the heterogeneous oxidative dehydrogenation of propane over hexagonal boron nitride. We apply a recently developed gas-phase combustion model for low-temperature combustion of propane and couple it with several surface microkinetic mechanisms to probe the selectivity limits using the open-source flame solver Cantera. We show that while the conversion of propane is surface-driven, the selectivities are significantly influenced by the gas-phase, especially when dilute catalyst beds are used.<br /> | Peter Kraus; R. Peter Lindstedt | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753f1337d6c0909e28939/original/it-s-a-gas-oxidative-dehydrogenation-of-propane-over-boron-nitride-catalysts.pdf |
60c74e14ee301c8a5cc7a42a | 10.26434/chemrxiv.12693458.v1 | Fick Diffusion Coefficients via Molecular Dynamics: An Alternative Approach in the Fourier Domain | Mutual diffusion coefficient data are required for several systems of scientific and engineering interest to properly describe mass transport phenomena over a wide range of pressures, temperatures, and compositions. In this work, we calculated Fick diffusion coefficients for some CO2+n-alkane mixtures at high pressures using a new method, which we derived by introducing modifications to the Fourier Correlation Method (FCM) originally proposed by Nichols and Wheeler [I&EC Research, 54, 12156–12164 (2015)]. The modified FCM (mFCM) results were validated through comparisons with experimental data and with Fick coefficients calculated by employing well-established Molecular Dynamics methodologies. The new approach has some interesting advantages, such as providing Fick coefficients for molecular systems directly through a single equilibrium calculation, in contrast to traditional methods in which an extra calculation is needed to obtain the so-called thermodynamic factor. It is shown that the new approach considerably reduces the finite-size effect of the simulation box on the calculated diffusion coefficients, which are thus obtained in the thermodynamic limit.<br /> | Thiago José Pinheiro dos Santos; Frederico W. Tavares; Charlles Abreu | Computational Chemistry and Modeling; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e14ee301c8a5cc7a42a/original/fick-diffusion-coefficients-via-molecular-dynamics-an-alternative-approach-in-the-fourier-domain.pdf |
60c742ee567dfe28b6ec3fd6 | 10.26434/chemrxiv.8852087.v1 | The Analysis of Dissolved Inorganic Carbon in Liquid Using a Microfluidic Conductivity Sensor with Membrane Separation of CO2 | Microfluidic lab on chip for measuring dissolved inorganic carbon with application to ocean chemical analysis and depth profiles. Miniaturised system using membrane separation of CO2 and concentration determination by conductivity for consideration on ocean autonomous floats.<br /> | Mark Tweedie; dan Sun; Durga Gajula; Brian Ward; PAUL MAGUIRE | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ee567dfe28b6ec3fd6/original/the-analysis-of-dissolved-inorganic-carbon-in-liquid-using-a-microfluidic-conductivity-sensor-with-membrane-separation-of-co2.pdf |
62e13867cf6612d63bb732f6 | 10.26434/chemrxiv-2022-d9gcs | In vitro Selection of an Aptamer Targeting SARS-CoV-2 Spike Protein with Nanopore Sequence Identification Reveals Discrimination Between the Authentic Strain and Omicron | DNA aptamers are oligonucleotides specifically bound to target molecules that can serve as antibodies of nucleic acid nature. For diagnosing the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), methods using antibodies specific to antigens on the virus are broadly used. We generated by classical SELEX a number of aptamers, interacting with the receptor-binding domain of SARS-CoV2 spike protein (SARS-CoV2 Spike RBD) from Wuhan-Hu-1 strain. The sequence identification was performed using a novel methodology based on the nanopore sequencing. For sequence identification of selected aptamers, we created the novel protocol for aptamer identification based on nanopore sequencing. We identified the best aptamer candidate named MEZ. It was chemically synthesized and tested for binding with SARS CoV2 Spike RBD domain of the S-protein from different strains. Kd of the complex is 6.5 nM being comparable with known aptamers. Virus neutralization tests demonstrate similar results for already known and MEZ aptamers. We identified differences for aptamers binding to SARS-CoV-2 Spike RBD from Wuhan-Hu-1 and Omicron strains. MD simulations reveal that the number of hydrogen bonds between the protein and aptamer is higher for the more stable complex. Moreover, dynamic network analysis show that the motions of the aptamer and protein are correlated to a higher extent in a more stable complex. Based on the experimental data and computational results we can conclude that the authentic RBD-aptamer complex has two specific points for interaction and the 3'-end of aptamer is responsible for strain identification. Therefore, the selected aptamer based on experimental data can be an alternative biological element for the development of SARS-CoV-2 diagnostic testing with strain specificity and cost efficiency due to the short length of aptamer being 31 nucleotides. | Maria Khrenova; Lyudmila Nikiforova ; Fedor Grabovenko; Nadezhda Orlova; Maria Sinegubova; Denis Kolesov ; Elena Zavyalova; Vera Spiridonova; Timofei Zatsepin; Maria Zvereva | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e13867cf6612d63bb732f6/original/in-vitro-selection-of-an-aptamer-targeting-sars-co-v-2-spike-protein-with-nanopore-sequence-identification-reveals-discrimination-between-the-authentic-strain-and-omicron.pdf |
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